Religious freedoms have been severely restricted in Crimea since it was annexed by Russia one year ago.
President Putin celebrated the anniversary yesterday with a parade outside the Kremlin, but Christian charity Release International reports that evangelical churches have been heavily restricted in the past year. There are now concerns for the future of Christians in Ukraine.
"After annexation, Ukrainian churches [were told] they had no right to exist there," one church leader, who has to remain anonymous for security reasons, said. "Every church has had to be re-registered. Some pastors and priests have been forced to accept Russian citizenship."
He said that those who refused citizenship were forced to leave, and added that evangelicals are seen as "dangerous" people, and as enemies of the state.
Muslims in Crimea, most of whom belong to the Tatar community, have also reported oppression.
The pastor warned that Ukrainian churches could also lose their freedoms if Russia manages to take control of parts of the country.
Parts of eastern Ukraine that have been occupied by separatists have already seen attacks on churches and church leaders.
"In the areas that have been occupied some Christians have been killed. They have been accused of being American spies," the pastor said.
The Institute for Religious Freedom (IRF), based in Kiev, has also recorded numerous act of persecution since the conflict began.
The IRF reports that that territories controlled by militants in Donetsk and Luhansk have seen a substantial increase in intolerance towards Christians, apart from those belonging Orthodox Church under the Moscow Patriarchate.
In May last year a Pentecostal pastor was beaten in Slovyansk, and in June four men were taken hostage from a Pentecostal church and shot the next day.
As in Crimea, they report that evangelical churches were the most frequent targets, including Pentecostals, Baptists, Adventists and charismatic churches, which together make up about a third of religious communities in the Donetsk region.
Release chief executive Paul Robinson said: "There has been a steady decline in religious freedom across the former Soviet Union in recent years. Separatists have killed Christians in the Ukraine, and the picture in the Crimea under Russian annexation paints a disturbing picture of the future for Christians in Russian-controlled territories.
"The idea that Christians who do not belong to the traditional Orthodox Church have embraced some form of pro-Western religion and could even be American spies is nonsense. Some other communist or post-communist countries make the same claim."