Ruslan Sokolovski is in detention for two months, a statement by the investigative committee said Saturday, and could face a five-year jail term if convicted.
On August 11, Sokolovski published a video on his YouTube channel showing him entering the Church of All Saints in Yekaterinburg and playing Pokemon Go on his iPhone throughout the cathedral.
“How can one offend by entering a church with a smartphone?” he said.
But investigators said searches on his home had shown evidence of incitement to hatred and attacks on the liberty of faith.
Authorities worldwide have issued a slew of warnings since the hugely popular smartphone app was launched in July.
It has already been blamed for a wave of crimes, traffic violations and complaints in cities around the globe.
The free app uses satellite locations, graphics and camera capabilities to overlay cartoon monsters on real-world settings, challenging players to capture and train the creatures for battles.
Pokemon has been popular in Japan since first being launched as software in 1996 for Nintendo’s iconic Game Boy console.