Habitat fragmentation threatens biodiversity worldwide, particularly affecting large-bodied species that require vast territories and move across long distances, including most large felids. The jaguar Panthera onca has lost more than half of its habitat throughout its range and its subpopulations are becoming isolated, making them susceptible to local extinction. Knowledge about the status of its subpopulations in highly fragmented environments is lacking but urgently needed. Using camera traps during 2019–2020, we estimated number of individuals, age classes and sex ratio, occupancy, relative abundance and density of jaguars in Nayarit, western Mexico. We also determined the relative abundance of potential prey and estimated the land-cover change rate during 1999–2019, using GIS. We found that a resident subpopulation of five adult females, two adult males and one cub, at a high density (5.3 individuals/100 km2), is supported by at least 14 wild prey species. Natural habitat in the area is rapidly decreasing because of expanding agriculture and shrimp farming: agricultural areas increased from 39 to 50% and mangroves decreased from 35 to 26% of the study area over 20 years. The high jaguar population density and the diversity and relative abundance of remaining wild prey are remarkable, considering that natural habitat in the area is highly fragmented, shrinking rapidly and embedded in a matrix of human-dominated land-cover types. Effective conservation actions are needed urgently, including the protection of patches with native vegetation, reforestation to maintain connectivity between these patches, and the involvement of local communities.