The Alto Mayo region in the Peruvian department of San Martin has one of the highest levels of deforestation and fragmentation in the country. Historically, San Martin was home to at least 20 primate species, of which at least 14 persist in the Alto Mayo Valley. We surveyed primate populations in the “Jungla de Los Monos”, a locally protected remnant of a naturally diverse primate community in one of the last remaining mid-elevation (800 m a.s.l.) seasonally flooded forests in the region. We recorded seven primate species, with a further two species reported to have been extirpated from the area. By far the most common species was Saimiri macrodon. Half of the primate biomass was made up of a single species, Alouatta seniculus, with S. macrodon accounting for another quarter. The endemic Plecturocebus oenanthe was only detected once in forest interior, but was observed in edge and riverine forest, as well as neighboring fragments. The area holds a surprisingly high diversity and density of primates considering its proximity to population centers, thanks primarily to self-imposed hunting bans and logging control by local communities.