All of the 226 mosques in Yala, more than 200 in Narathiwat and over 700 in Pattani opened their doors to devotees after the Sheikhul Islam Office issued guidelines for Eid al-Fitr celebrations.
Muslims usually gather to catch sight of the moon, which marks the end of the fasting month.
Most mosques have asked people to register, but it is expected that the number of people attending prayers will be far larger than expected.