By CLIFFORD J. LEVY

STARY OSKOL, Russia - It was not long after a Methodist church put down roots here that the troubles began.
First came visits from agents of the F.S.B., a successor to the K.G.B., who evidently saw a threat in a few dozen searching souls who liked to huddle in cramped apartments to read the Bible and, perhaps, drink a little tea. Local officials then labeled the church a “sect. Finally, in March, they shut it down.
There was a time after the fall of Communism when small Protestant congregations blossomed here in southwestern Russia, when a church was almost as easy to set up as a store. Today, this industrial region has become emblematic of the suppression of religious freedom under President Vladimir V. Putin.
Just as the government has tightened control over political life, so, too, has it intruded in matters of faith. The Kremlin’s surrogates in many areas have turned the Russian Orthodox Church into a de facto official religion, limiting other Christian denominations that seem to offer the most significant competition for worshipers. They have all but banned proselytizing by Protestants and discouraged Protestant worship through a variety of harassing measures, according to dozens of interviews with government officials and religious leaders across Russia.

Religious Intolerance
This close alliance between the government and the Russian Orthodox Church has become a defining characteristic of Mr. Putin’s tenure, a mutually reinforcing choreography that is usually described here as working “in symphony.
Mr. Putin makes frequent appearances with the church’s leader, Patriarch Aleksei II, on the Kremlin-controlled national television networks. The relationship is grounded in a nationalistic ideology dedicated to restoring Russia’s might after the disarray that followed the end of the Soviet Union. The church’s hostility toward Protestant groups, many of which are based in the United States or have large followings there, is tinged with the same anti-Western sentiment often voiced by Mr. Putin and other senior officials.
The government’s antipathy also seems to stem from the Kremlin’s wariness toward independent organizations that are not allied with the government.
Here in Stary Oskol the police evicted a Seventh-day Adventist congregation from its meeting hall, forcing it to hold services in a ramshackle home . Evangelical Baptists were barred from renting a theater for a Christian music festival, and were not even allowed to hand out toys at an orphanage. A Lutheran minister said he moved away for a few years because he feared for his life. He has returned, but keeps a low profile.

A New Identity
On local television in March, the city’s chief Russian Orthodox priest, who is a confidant of the region’s most powerful politicians, gave a sermon that was repeated every few hours.
His theme: Protestant heretics.
“We deplore those who are led astray - those Jehovah’s Witnesses, Baptists, evangelicals, Pentecostals and many others who cut Christ’s robes like bandits, who are like the soldiers who crucified Christ, who ripped apart Christ’s holy coat, declared the priest, the Reverend Aleksei D. Zorin.
Such language is familiar to Protestants in Stary Oskol, who number about 2,000 in a city of 225,000.
The Reverend Vladimir Pakhomov, the minister of the Methodist church, recalled a warning from an F.S.B. officer to one of his parishioners: “ ‘Protestantism is facing difficult times - or maybe its end.’
Most Protestant churches are required under the law to register with the government to do anything more than conduct prayers in an apartment. Officials rejected Mr. Pakhomov’s registration this year, first saying his paperwork was deficient, then contending that the church was a front for an unspecified business.
Mr. Pakhomov appealed in court, but lost. He said he could face arrest for so much as chatting with children about attending a Methodist camp.
“They have made us into lepers to scare people away, Mr. Pakhomov said. “There is this climate that you can feel with your every cell: ‘It’s not ours, it’s American, it’s alien; since it’s alien we cannot expect anything good from it.’ It’s ignorance, all around.
Yuri I. Romashin, a senior city official, said the denial of the Methodist church’s registration was appropriate, explaining that the government had to guard against suspicious organizations that used religion as a cover. “Their goal was not a holy and noble one, he said of Mr. Pakhomov’s church.

In the Grip of Orthodoxy
The limits on Russia’s Protestants - roughly 2 million in a total population of 142 million - have by no means reached those that existed under the officially atheistic Soviet Union .
The Russian Constitution guarantees freedom of religion, and Mr. Putin has often spoken against discrimination. He has also denounced anti-Semitism. While many Jews have emigrated over the past two decades, the Jewish population - now a few hundred thousand people - is experiencing something of a rebirth here. Anti-Semitism has not disappeared. But in some regions it seems to have been supplanted by anti- Protestantism and, to a lesser extent, anti- Catholicism.
Mikhail I. Odintsov, a senior aide in the office of Russia’s human rights commissioner, said most of the complaints his office received about religion involved Protestants.
Mr. Odintsov listed the issues: “Registration, reregistration, problems with property illegally taken away, problems with construction of church buildings, problems with renovations, problems with ministers coming from abroad, problems with law enforcement, usually with the police. Problems, problems, problems and more problems.
“In Russia, he said, “there isn’t any significant, influential political force, party or any form of organization that upholds and protects the principle of freedom of religion.
While church attendance in Russia is very low, polls show that Russians are embracing Russian Orthodoxy as part of their identity. In one recent poll, 71 percent of respondents described themselves as Russian Orthodox, up from 59 percent in 2003.

‘American Faith’
Here in southwestern Russia, the Belgorod region, traditionally a stronghold of Russian Orthodoxy, has been at the forefront of the anti-Protestant campaign.
In 2001, during Mr. Putin’s first term, the region enacted a law to drastically restrict Protestant proselytizing. More recently, it mandated that all public school children take what is essentially a Russian Orthodox religion course.
Archbishop Ioann, the chief Russian Orthodox priest in the Belgorod region, said Russians had a deep connection to Orthodoxy that the government should nurture.
The archbishop denied that the church disparaged Protestants.
“In our sermons, you will never hear us trying to condemn them or say that they do anything wrong, he said. In fact, on the day the archbishop was being interviewed, local television was repeatedly showing the sermon of his deputy, Father Zorin, likening Protestants to those who killed Jesus Christ.
Protestants here must receive official permission before doing anything remotely like proselytizing.
The Reverend Vladimir Kotenyov, a Baptist minister, said his church had given up asking. “Naturally, it will be perceived as propaganda directed at our population, Mr. Kotenyov said. “ ‘What kind of propaganda are you preaching-’ they would ask.
‘An American faith?’
“This is how they think: If you are a Russian person, it means that you have to be Russian Orthodox.