The song outraged the Russian Orthodox Church. It accused them of blasphemy.
Supporters say the case reflects the state’s growing intolerance of government opponents.
Nadezhda Tolokonnikova, Maria Alyokhina and Yekaterina Samutsevich caused outrage when they sang a song that implored the Virgin Mary to “throw Putin out” in February.
The head of the Russian Orthodox Church, Patriarch Kirill, has said the performance, which took place at the altar of Christ the Saviour Cathedral, amounted to blasphemy.
The women are facing the charge of hooliganism motivated by religious hatred or hostility and could face up to seven years in prison.
Pussy Riot made headlines around the world late last year when footage of their controversial public perfomances at Moscow landmarks such as Red Square attracted millions of viewers on the internet.
More than 100 prominent Russian actors, directors and musicians have urged the authorities to release the three.
Western musicians such as Sting and the Red Hot Chili Peppers have also criticized the women’s arrest.
Activists have said the case indicates that President Putin, now serving a third term in office, is not heeding calls for him to be more tolerant of political opponents.
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