Although tropical forest vertebrate populations are often heavily impacted by both habitat loss and subsistence hunting, in many human-dominated landscapes their fate depends on the wider habitat matrix outside protected areas. This study used line-transect surveys to examine patterns of vertebrate species richness and encounter rates (ER) throughout Mexico's Yucatan Peninsula across a broad spectrum of anthropogenic forest disturbances. Censuses were carried out at eight forest sites, including two localities within the Sian Ka'an Biosphere Reserve, a communally managed protected area, a private forest reserve and three communal-tenure landholding units. Species richness increased with increasing forest cover in the surrounding landscape, but was not affected by the degree of hunting pressure. Responses to different forms of disturbance varied markedly across species and functional groups. Aggregate ER of old-growth specialists were positively correlated with forest cover, but unrelated to hunting pressure. Hunting pressure was strongly related to aggregate ER of game species, particularly of preferred prey, and a meta-analysis of species-specific correlations showed a significant effect of hunting pressure on the ER across individual game species. Sampling within old-growth forest of Sian Ka'an yielded relatively high ER for almost all species. In comparison, low ER were obtained for several species at Sian Ka'an sites consisting of a higher proportion of open habitat. Landholding units showed low relative abundances, but species ER varied depending on disturbance type. The communally managed reserve exhibited high ER for both game and non-game species. Synthesis of these results with comparable data from 19 additional Mesoamerican sites shows that species-specific ER found across the Yucatan Peninsula are within the ranges observed elsewhere, with a consistent pattern of lower abundances in hunted sites. It is critical that private, communal and public-sector reserves are integrated into a coordinated management approach across the wider landscape in this biodiversity hotspot and throughout the Mesoamerican Biological Corridor.