Kampala is a city of clamor. Uganda’s capital, a metropolis of 1.2 million, lies in the rolling highlands surrounding Lake Victoria. The acoustics of the place are such that sounds rise to wash over its green hills like a gentle tide. Climb one of them any Sunday and listen, and up will waft Uganda in all its varied devotion: a muezzin’s call to prayer, an Anglican hymn, the gravelly bark of a born-again preacher – “Ha-lle-luiah!”The Church of St. Nicholas stands atop a hill called Namungoona on the outskirts of Kampala, up a winding dirt road from an open-air evangelical congregation and a Catholic church shaped like a pagoda. St. Nicholas’s is prim and yellow, with a peaked roof and windows of brightly colored stained glass.

On a recent soggy Sunday, worshipers filed inside to the clank of a bell, taking care as they entered to kiss a gold-bound copy of the Gospels that lay on a pedestal near the door. At the front of the church, before icons of Jesus, Mary and the congregation’s patron saint, stood a gray-bearded man bedecked in white vestments and a jeweled crown. He was Jonah Lwanga, Metropolitan of Kampala and All Uganda, and crammed into the rows of wooden pews before him, singing heartily in the local language, Luganda, was one of the most unlikely congregations in a nation renowned for its religious diversity. They were African followers of the Orthodox Church.

Orthodox Christianity is not new to Africa. According to tradition, the Evangelist Mark arrived on the continent around A.D. 43, and founded the Church of Alexandria and, by extension, all Africa. But “all Africa,” for most of the church’s history, effectively ended at the Sahara. Orthodox missionaries sat out the 19th century’s “scramble for Africa,” when European Catholics and Protestants fanned out across the continent to save souls and build colonies. The story of how the Alexandrian Church came to have an affiliate in faraway Uganda, a country with no previous connection to the Orthodox world, is therefore not a tale of white men bearing the message of God to a dark continent. Rather, the Ugandan church traces its roots to two Africans who, rebelling against colonial rule, fled to a religion they felt was pure and politically uncompromised. This makes Uganda’s small community of 60,000 Orthodox Christians nearly unique within their home country. They found their faith on their own.

Metropolitan Jonah, 62, whose rank in the Orthodox hierarchy is roughly equivalent to a Roman Catholic archbishop’s, is currently the only black African member of the synod of the Orthodox Patriarchate of Alexandria, which is dominated by men of Greek descent. The grandson of one of the church’s founders, he exemplifies the divided nature of his community. Equally comfortable speaking Greek as he is English or any number of African languages – he studied at a seminary on Crete and at the University of Athens – the metropolitan, nonetheless, says he has encountered “great, great difficulties” in convincing some Orthodox that his church really belongs to their tradition. But he believes that somehow, over 80 years of struggle in a country where life is hard, his church has managed to become something both fully African and authentically Eastern.

That morning at St. Nicholas’s, the smell of incense clung to the air as Metropolitan Jonah appeared from behind the iconostasis – the icon-decorated wall separating the altar from the congregation in many Eastern churches – carrying a pair of silver candelabras, one with three flames, one with two, meant to signify the Trinity and the dual nature of Christ. “Ayi Mukama, ayi Mukama,” he prayed in Luganda – “O Lord, O Lord” – as he moved the candles in fluid rotations. The metropolitan chanted a psalm calling on God to “look down from heaven and behold” a community he had planted like a vineyard. Then he repeated the prayer – this time in Greek.

Uganda has always been fertile ground for religion. Islam arrived in the middle of the 19th century, brought by Arab traders from the Swahili coast doing business in slaves. Anglicans of the Church Missionary Society arrived in 1879, and the White Fathers came a year later. The European missionaries braved hard journeys, malaria and incalculable danger – in the early years, several were killed in tribal wars or intrigues at the thatch-roofed court of the kabaka, the king of the dominant Baganda tribe – to “plant churches of the living God in Central Africa,” as one of them put it.

After a little initial resistance, the missionaries’ message was embraced. Then, with the zeal of the converted, Uganda’s Catholics, Protestants and Muslims fell into a series of religious wars. The British sided with the Protestants. When the smoke cleared, the kabaka was Queen Victoria’s subject, Uganda was a protectorate and Anglicanism was the de facto state religion.

From the beginning, there were always some who rebelled against the government and its established faith. Reuben Spartas, the father of the Ugandan Orthodox Church, was one such dissenter. Spartas was born Reuben Mukasa in a village near Kampala in 1899, around the same time his land was losing its independence. He acquired the name he was to carry for the rest of his life at an Anglican mission school, where his discipline and athleticism reminded his classmates of the Spartans of their history books.

When World War I broke out, Spartas served in the British Army as a hospital orderly. But he was a fierce nonconformist, and before long he had joined the movement against British rule in his country. Spartas founded several short-lived nationalist organizations, with names like the African Progressive Society and the Christian Army for the Salvation of Africa. He joined a political party that agitated for the land rights of dispossessed Bagandan tribes, winning the notice of colonial authorities who judged him “an eloquent and powerful speaker” and eventually threw him in jail for a time.

Spartas was, in short, a man in search of a vehicle for his nationalist passions. As it turned out, that vehicle was to be a church. He was a devout man, but by the mid-1920’s Spartas had grown increasingly frustrated with what he saw as the established church’s compromises and inconsistencies. He and an army buddy, Obadiah Basajjakitalo – Metropolitan Jonah’s grandfather – began exploring other religions. What happened next has taken on the air of a creation myth: Spartas supposedly ran across an entry for the word “Orthodox” in the dictionary. “Like another Archimedes,” a subsequent church leader wrote, “he ran out into the streets shouting: ‘I have found, I have found!’ ”

The real story is a bit more complicated, involving an iconoclastic early civil rights leader and a case of mistaken religious identity. Sometime in the 1920’s, Spartas got hold of a copy of a newspaper called the Negro World, which was published by Marcus Garvey, the West Indian progenitor of the “back to Africa“ movement. Spartas learned that Garvey had championed the creation of an African Orthodox Church. Other than sharing a name, Garvey’s church had no relationship to mainstream Orthodoxy. But Spartas did not know that. In 1925, he wrote African Orthodox Church leaders in America, saying he wanted to join up and convert other Ugandans.

After a long courtship-by-letter, Spartas announced that he had left the Anglican Church and declared the establishment of a new church “for all right-thinking Africans, men who wish to be free in their own house, not always being thought of as boys.” In 1932, one of Garvey’s bishops traveled to Uganda and ordained Spartas and Basajjakitalo priests. The kabaka of Baganda donated a section of his personal estate at Namungoona to the new church, and within a few years, it claimed 5,000 members.

There was just one problem – the church was not really Orthodox. Spartas discovered this when a Greek expatriate in town came to baptize a child and told him he had the rituals all wrong. Worried correspondence with Alexandria ensued and, after some confusion, all links to Garvey’s church were severed, and Spartas traveled to Egypt to be ordained by Patriarch Christophoros II. The Ugandan Orthodox had Alexandria’s recognition. Acceptance would be longer in coming.

One weekday afternoon, Metropolitan Jonah welcomed me into the sitting room of his home in Namungoona, which stands near a giant gnarled mango tree just across the way from St. Nicholas’s. The room is simple by an archbishop’s standards, paneled with dark wood and crammed with plush furniture in the Ugandan fashion. On its walls hang Greek icons and numerous portraits of bearded Orthodox Church leaders, both white and black. The metropolitan, a man of regal carriage and a honeyed baritone voice, wore a simple black cassock and an engolpion, an ornate medallion that all Orthodox prelates wear around their necks. In order to tell me the story of his church, he took me on a tour of what was hanging on his walls.

He stopped before a faded black-and-white photograph of a slight, elderly man. It was his grandfather, he said, Basajjakitalo, a beloved figure known in his old age as “Father O.K.”

“They had seen the conflict between the Catholics and the Protestants, and they were asking, ’Why, when the Bible is one?’ “ the metropolitan said. “Then they saw there is an original church where the two bodies were coming from: the Orthodox Church. And for them, they said, ’We will join the original one.’ ”

Metropolitan Jonah pointed to the portrait next to Basajjakitalo’s, a painting of a man wearing sunglasses and a beatific smile. “That is Theodoros,” he said, Spartas’s successor and his own predecessor as leader of the Ugandan community. The metropolitan told me that Theodoros was the first Ugandan to join the Alexandrian synod in 1995. “After being an auxiliary bishop for 45 years,” he added, cracking a wry smile.

Uganda’s Orthodox have gotten used to waiting. Though their church won official recognition from Alexandria in 1946, the first full-time Greek Orthodox missionary did not arrive in the country until more than a decade later. As of 1957, Spartas and Basajjakitalo were still the only two Ugandan priests – serving more than 50 parishes nationwide – and the Greek bishops appeared to be in no hurry to ordain more.

Wealthy Orthodox congregations overseas have given some financial assistance through the years – Greeks donated most of the icons and other fixtures in the church – but the patriarchate itself always had priorities other than Africa. During the 1970’s and 1980’s, as the country endured dictatorships and civil wars, an increasing number of Ugandans abandoned mainline religions for homegrown evangelical churches, and the Orthodox community suffered.

“We lost very many because there were no priests to handle the responsibility,” Metropolitan Jonah said. “The communities were dissolving.”

Change began in the mid-1980’s, when a new archbishop was assigned to East Africa. He opened a seminary in Kenya, home to 60,000 Orthodox faithful, about the same as in Uganda, according to church officials. (There are smaller Orthodox populations in Cameroon, Ghana, Madagascar, Nigeria, Tanzania, Zaire and Zimbabwe.) The archbishop ordained many priests and cultivated new leaders – including Metropolitan Jonah.

In the early 1990’s, Parthenios III of Alexandria became the first patriarch to visit Uganda, and the experience prompted him to “make some radical changes,” said Metropolitan Jonah. In the eight years since he ascended to the rank of metropolitan, “something has happened that is really fantastic,” he said. “When you are able to move around a little bit …this is when you might even be able to get support.”

Metropolitan Jonah has high hopes for Alexandria’s new patriarch, Theodoros II, a Cretan who previously served as a bishop in Cameroon and Zimbabwe. Still, the metropolitan said he had never been able to escape the sense that some of his peers view him and his church as not “Greek” enough. “I am alone in the Holy Synod as a black man,” he said. “You can understand the difficulty I have.”

Recently, Uganda has enjoyed relative stability and prosperity, and the Orthodox Church, like the country itself, has enjoyed something of a resurgence. In Namungoona, a primary and secondary school each have around 500 students, and there is a 40-bed hospital, maintained with help from Greece. But the church’s reach extends throughout the country via a network of parishes and schools, located in places as wretched and remote as a camp for refugees displaced by a long-running civil war in the north.

“One of the things about our parishes is that almost every one of them seems to be at the very end of the road,” said Peter Georges, a missionary from Ohio who has been living on-and-off in Namungoona since 2002.

The future of the church, however, can be said to lie much closer to home, in a low-slung dormitory across a courtyard from Metropolitan Jonah’s residence. There, 15 young seminarians study to become priests. When they are ordained, they will increase the number of Orthodox priests in Uganda by 50 percent – though the metropolitan says he still needs many more. In a country where the youth increasingly gravitate to the balokole (born-again) movement, with its charismatic preachers, upbeat songs and promises of miracles, these young men stand apart.

“There are some [Orthodox] youth who have gone over to the balokole, but few,” Metropolitan Jonah said. “I would say those are the Africans who are very taken with the songs and dances. But we say life is a very serious business. People who are serious, they are going to receive the message.”

Andrew Rice has written about Africa for The New York Times Magazine, The Nation and The New Republic among others. Photographer Tugela Ridley is based in Kampala.