For the past week, people have been pulled from cars by gangs and stabbed. Murdered for having the wrong religion on their identity cards. Police say that at least 65 people have been killed, with another 62 in hospital. Unofficial totals go up to 200.
An uneasy lull has now settled, although there are daily reports of violence on nearby islands. Only a handful of shops are open. People leave their homes only to look for food.
In Ambon city, epicentre of the killing, soldiers armed with ageing rifles guard every street, but admit, privately, that they cannot stop the violence if it flares up again.
"It is quiet, but it's not under control. Violence could break out at any time. There's a feeling of vengeance because so many people died," says a Dutch journalist in Ambon, once a base for Holland's spice-trading empire.
Most Ambonese are Christians, and many of the victims were Muslim immigrants from the nearby island of Sulawesi.
Most of Indonesia's 200 million people are technically Muslims, though many are not devout. The country has a reputation for being more tolerant than some other big Asian countries with a mix of religions, such as India and Pakistan. Yet since the fall of President Suharto last May, that reputation has started to unravel.
There have been smaller communal riots in recent weeks on other Indonesian islands, including Timor, Sulawesi and Sumatra. Seven people, most of them Ambonese gangsters, were butchered by Muslims in Jakarta in November. It isn't clear yet if revenge for these deaths is a factor in the violence. The police say that hoodlums from Jakarta may be involved, but the investigation is going on. The violence in Indonesia is not as widespread as some foreign news reports suggest. Most areas of this vast archipelago are still peaceful. But the problems are likely to get worse.
The first free elections in 40 years are due to be held on 7 June, and many people fear bloodshed as more than a hundred parties jostle for support. An economic crisis has driven millions of people into poverty, and street crime is rising.
Many people say that elements of the old Suharto regime are stirring up the riots because they fear being called to account for misuse of power.
The former president is being investigated for corruption. He still has many loyalists in the army, the bureaucracy and the criminal underworld.
Abdurrahman Wahid, an influential and outspoken Muslim leader, went to see Suharto on Wednesday night at his Jakarta mansion. "I asked him to use his influence to stop his followers from causing a commotion which could disrupt the elections, including the Ambon case and riots in other areas," he said. It was not clear what answer he got.
Much depends on what the armed forces do. The soldiers, divided and unpopular, have been unable to stop the riots. Their commander, General Wiranto, is both a cautious reformer and a protege of Suharto.
"I think we are nearing the point where Wiranto will have to make a break with his past and clamp down on Suharto's old guard," says Marzuki Darusman, who heads the government's human rights team.