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A violent protest against Jakarta Governor Basuki Tjahaja Purnama on Friday is the latest sign of rising religious intolerance in the world’s most populous Muslim-majority nation. The Islam Defenders Front and other Islamist groups rallied 200,000 followers in the capital to demand the Christian and ethnically Chinese Mr. Purnama be imprisoned for blasphemy. That’s a show of strength that will only grow if Indonesia’s political and religious leaders don’t stand up to it.

Islamists misquoted a September speech in which Mr. Purnama cited the Quran and started a social-media campaign against him. He has since apologised, and a police investigation is expected to clear him. But the accusation led to Friday’s rally, at which participants openly incited violence against the Governor. Some protesters burned cars and looted shops.

Mr. Purnama, who has been the target of assassination plots in the past, is running for re-election in February. His chances are good since he remains popular with Jakarta’s population, especially the middle class. Originally, Deputy Governor, he took over when his predecessor, Joko Widodo, won election as Indonesia’s President in 2014. He continued Mr. Widodo’s work of improving city services and rooting out corruption.

But Mr. Purnama’s religion and ethnicity make him a target for Islamists. In recent days anti-Chinese posters and graffiti have appeared in Jakarta, bringing back memories of 1998 riots in which hundreds of ethnic Chinese were killed. Radical groups called on their supporters to use last week’s protest to incite jihad across the country. That is a real danger, as attacks on Christians and other religious minorities have increased.

Much of the blame lies with former President Susilo Bambang Yudhoyono, who endorsed fatwas of the Indonesian Ulema Council, a group of top clerics, against minorities. The Defenders Front was allowed to operate with impunity even though it was linked to the burning of churches and attacks on Ahmadiyya Muslims. Mr. Yudhoyono, whose son is running against Mr. Purnama, said he supported Friday’s protest “300%.”

Indonesia successfully cracked down on the Islamic terrorist group Jemaah Islamiyah after the 2002 Bali bombings that killed 202 people. But successive administrations left intact the wider ecosystem of radical Islam, much of it financed with Saudi money, that incites violence against minorities. In January an Islamic State-affiliated group killed four people in an attack in Jakarta.

Mr. Widodo represents a modest improvement on his predecessor since he at least speaks out against attacks on minorities. Yet he too has failed to tackle the rise of extremist ideology, and the number of attacks continues to rise. The Setara Institute, an Indonesia human-rights group, reported 236 cases of religious violence in 2015, up from 177 in 2014.

Indonesia’s traditional, more tolerant form of Islam still enjoys strong support. It’s encouraging that the country’s largest mainstream Muslim groups, Muhammadiyah and Nahdlatul Ulama, urged their members to stay away from Friday’s protests.

Indonesians will nonetheless have to do more to resist the pull of Islamic radicalism. Mr. Purnama’s fate represents an important test of the country’s record of religious tolerance and secular government.

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