Habitat loss and fragmentation in tropical regions are major threats to the persistence of endangered Malay tapir (Tapirus indicus). The Malay tapir distribution is largely constrained to fragmented habitats inside protected areas. However, it is unclear how the spatial patterns of habitat fragmentation affect its relative abundance. Here, we investigated the effects of habitat fragmentation on Malay tapir relative abundance in Thailand. We first quantified the spatial patterns of habitat fragmentation within nine of Thailand’s protected areas. Second, we assessed the relationship of fragmentation metrics and relative abundance of Malay tapirs. Third, we identified the relative importance of the fragmentation metrics in explaining relative abundance. We found that tapir abundance remained unexpectedly high in the Southern forest complex despite the fact that tapir habitats were significantly more fragmented there than in the protected area in the western forest complex (p < 0.05). Additionally, we found a significantly negative relation with clumpiness index (R2 = 0.51, p < 0.05). This suggests that other factors may also be influencing their populations, so that the Southern protected areas provide preferred habitat with higher relative proportions of moist evergreen forest, large habitat patch size, precipitation, and elevation. It highlights the importance of interconnected habitat for tapirs, and the benefit of conservation efforts in small, less recognized protected areas.