Quaternary small mammals are important proxies for paleoenvironmental reconstructions. The Brazilian record, although famous and continuously growing, is hampered by poor chronological control due to the nature of most of the published assemblages. Here, we present a taphonomic analysis and paleoenvironmental reconstruction based on marsupials, bats, and rodents (480 remains) from the Gruta do Presépio archeological site (GPR, hereafter), Santa Catarina State, southern Brazil. The site is a rock shelter located in an Atlantic Forest biome, an important biodiversity hotspot. The GPR sedimentary sequence spans the Early Holocene (8330 ± 30 years 14C BP) to recent Historical time (after the arrival of Europeans). Most of the small mammal remains were deposited by strigiforms, although for the oldest units some strongly digested remains could indicate the activity of diurnal birds or carnivorous mammals. The GPR small mammal assemblages include 28 taxa (five marsupials, nine chiropterans, and 14 rodents). Most of them indicate the occurrence and persistence of forested environments during the Holocene around the site, which is in overall agreement with regional palynological data. A major community change, implying the increment of rodents allied to disturbed ecosystems (e.g. Akodon, Oligoryzomys, Mus), is very recent and reflects human forest clearance as a signature of the Anthropocene.