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It is currently housing 914 prisoners, including the Villager from the Animal Crossing series, who in this series is a dangerous psychopath and also a serial killer. However when the Villager escaped, the counter became 913.
Before that it had 916 prisoners including Mario and Toad. In SM64: ṩṩἔᾗмὄḋᾗᾄʀ 7 (TOAST edition), Shy Guy got mistakenly arrested due to a Toad mistaking the Shy Guy playing with another Toad as buttsex, which added to the counter and resulted in 915 prisoners. In "SM64 Bloopers: Can the Villager come out to play?", Princess Peach had been arrested by MM54321. With Peach and Shy Guy arrested altogether MMMP is now housing 915 prisoners (916 if you count Villager).