At the break of dawn, the fertile plain of Mrauk U, on a remote river in western Myanmar (Burma), is an archaeologist's dream come true.

The sun washes over hundreds of medieval temples, pagodas, and palaces. This is the lost capital of a fabled empire. Here the powerful kings of Arakan commanded the trade routes of South Asia from a city of 20 square miles (52 square kilometers) and 160,000 inhabitants. Today plowmen silently guide their water buffalo through verdant rice paddies, and cows wander the grounds of 600-year-old monasteries. ( Read about the race to save architecture in Myanmar's biggest city .)

But the dreamlike calm of Mrauk U cloaks a 21st-century nightmare. Myanmar's Rakhine region, where the ancient city lies, is the scene of relentless ethnic cleansing directed at a Muslim minority known as the Rohingya—deemed "illegal migrants," without citizenship or rights, after generations of residence.

Since 2012, when the crisis escalated into savage violence, Rohingya neighborhoods in Sittwe, the modern capital of Rakhine, have been burned to the ground. Tens of thousands have fled in flimsy wooden boats, only to be turned away by neighboring countries. Human traffickers demand extortionate fees for their services, and summarily kill any who are unable to pay.

View Images Though many Rohingya have lived in Myanmar for generations, they are considered illegal aliens from Bangladesh and forced to live in squalid camps, such as this one north of Sittwe. Photograph by Adam Dean, Panos

More than 140,000 Rohingya refugees are locked up in a single fetid concentration camp overseen by the Myanmar government. Much of the state has been closed to international aid workers and journalists.

The assault has been led by nationalist political parties and Buddhist monks, joined in a coalition known as the Race and Religion Protection Association. ( Read about how China's thirst for energy is threatening Myanmar's villages. )

"These hatemongering groups maintain close allegiances with senior government officials and have successfully influenced the passing of discriminatory legislation," says Khin Ohmar, a democracy activist who was a key figure in the 1988 uprising against the military in Myanmar.

Watch: Journey to the ancient religious complex of Angkor Wat in the jungles of Cambodia. A "city of temples" that reveals itself through a vast labyrinth of carved facades, galleries, and stairways.

The legislation's ostensible purpose is to eliminate an "alien threat" to the nation's Buddhist-dominated cultural traditions and religious legacy.

Yet the documented history of Mrauk U shows that Islam—and the ancestors of many Rohingya families—have played key roles in Rakhine's cultural life for centuries. In the golden age of Arakan, its Buddhist monarchs presided over a uniquely cosmopolitan realm of Muslim intellectuals and merchants, Portuguese Christian mariners, and Hindu artisans, all living side by side with Buddhist aristocrats and warriors. ( Read about poaching and wildlife trafficking in remote areas of Myanmar.)

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Empire of Tolerance

The assault on the Rohingya would have seemed incomprehensible to King Min Saw Mon Narameikhla, who established Arakan's Mrauk U dynasty in 1430 and built a stunning new city there as his capital.

View Images Intercepted by border guards while trying to cross into neighboring Bangladesh, Rohingya women and children await their fate. Photograph by Munir Uz Zaman, AFP/Getty

Known also by the honorific Islamic title Sulaiman Shah, the king had spent two decades in exile in the Muslim sultanate of Bengal. His policies and governing customs were oriented toward his Muslim allies on the Indian Ocean rather than to hostile Buddhist principalities to the east. Nearly all Min Saw Mon's successors over the following three centuries followed his lead.

As Rohingya historian Mohammad Yunus points out, the Buddhist kings of Arakan minted coins with trilingual inscriptions, in Arakanese, Bengali, and Arabic, bearing the Islamic profession of faith: "There is no god but Allah, and Muhammad is his prophet."

At its peak, Arakan was a leading maritime power, flaunting its wealth in a spectacular building spree. Within a few decades of its establishment, Mrauk U's only architectural rivals in Southeast Asia were Bagan, in central Burma, and Cambodia's Angkor Wat, both of which were abandoned by then. In the words of a 1996 UNESCO report, the city's monuments from that period "have no equivalent in the region."

View Images Forced to leave their homes as a result of violence, refugees live in makeshift shelters in a camp in Sittwe, Myanmar. Photograph by Jonas Gratzer, LightRocket/Getty

The centerpiece of old Mrauk U is Shitthaung Temple, the "pagoda of 80,000 Buddhas." Its three stories of intricately carved corridors are adorned by 547 sculpted poems dedicated to Buddha's reincarnations and a dizzying succession of images of the Buddha. On the eastern edge of the city stands the Santikan Mosque, the city's most important center of Islamic worship. It was built in the 1430s by Min Saw Mon.

Filling the valley floor and topping its hills rise spires and domes almost too numerous to count, necklaced by a phenomenal system of irrigation canals and artificial lakes that testifies to ancient Arakan's highly advanced engineering. Mrauk U in 2015 is filled with scenes of ancient life—there are no cars in the small town. Yoked oxen and horse-drawn buggies ply the unpaved roads.

Rewriting History

It can seem like a paradise of tranquillity to a visitor from the hectic urbanized West. But just a 15-minute walk from Shitthaung Temple and Santikan Mosque are the offices of the Rakhine Nationalities Development Party, which has incited much of the ethnic cleansing.

View Images A Rohingya father and son survey the ruins of their neighborhood following violence that erupted in 2013. Many Rohingya enclaves have been destroyed. Photograph by Jonas Gratzer, LightRocket/Getty

"The Rohingya are a dirty, thieving people who steal from the Burmese. They should be sent back where they came from," a local businessman says, using the familiar vocabulary of racial xenophobia heard everywhere.

Most scholars concur that the racial demography of Rakhine was in fact overwhelmingly Indo-Aryan rather than Burmese for the first 2,000 years of its recorded history. There is considerable evidence that the Rohingya trace their ancestry to this community. In 1901, under the British raj, a census found that 21 percent of Rakhine's people were Muslim. According to the Brussels-based International Crisis Group, Muslims constituted 30 percent of the state's 3.2 million population prior to the 2012 riots.

In an official compilation of Myanmar's ethnic groups, the government lists 135 communities. The Muslims of Rakhine are not among them. "The history of the Rohingya people in Burma has been wiped out for decades," says Khin Ohmar, who now serves as coordinator of Burma Partnership, an advocacy organization. Like many opposition activists, she refers to her country by its name prior to military rule.

View Images Built in the 1530s, Shitthaung Temple is Mrauk U's most famous attraction. Its mazelike corridors are adorned with countless depictions of the Buddha. Photograph by Luca Tettoni, Robert Harding World Imagery/Corbis

Nobel Peace Prize laureate Aung San Suu Kyi, the leader of the opposition and a candidate in next October's presidential elections, has made no public comment on the Rohingya's erasure from the map. Given the surge of xenophobic nationalism, "it is politically dangerous to support the Rohingya," notes Ohmar. But "it is disappointing for the human rights community to see [Suu Kyi] remain silent," she adds.