In order to prioritize the conservation and management efforts to protect jaguars (Panthera onca), it is of utmost importance to determine their tolerance in face of human disturbances, habitat modifications and varying degrees of prey availability. We assessed the occupancy probability of jaguars and five of their most common prey species throughout a heterogeneous landscape in the Selva Maya in southern Mexico: armadillo (Dasypus novemcinctus), coati (Nasua narica), paca (Cuniculus paca), white-tailed deer (Odocoileus virginianus), and collared peccary (Dicotyles tajacu). Additionally, we projected prey and Jaguar occupancies onto a 5993 km2 landscape based on the habitat type in the area. We averaged the best prey models ranked by QAICc and found that white-tailed deer had the highest average occupancy probability of 0.72 ± 0.06 and paca the lowest with 0.14 ± 0.04. The average occupancy probability for jaguars was 0.35 ± 0.07 and the strongest predictor of jaguar occupancy was a positive effect of collared peccary occupancy. These findings support previous studies that show that predator distribution is largely influenced by their prey availability, even in the midst of degraded habitats, and underlies the essential need to incorporate protection plans for prey species in jaguar conservation strategies.