Studies of Taiwanese mammals reveal varied patterns of population divergence. Low-mobility species such as mole-shrews and Formosan wood mice exhibit strong north–south splits. Surprisingly, similar patterns also occur in mobile taxa like Formosan serow and sambar deer. In contrast, other mobile species, including flying squirrels, and Reeves’s muntjac, show weak or no population structure. This recurring north–south divergence across taxa with diverse ecologies suggests that shared environmental and geographic gradients, in addition to historical isolation, may underlie these patterns. If so, species occupying similar habitats may exhibit comparable genetic breaks regardless of life history traits. Prior studies based solely on mitochondrial DNA may have missed fine-scale structure in species like muntjac; high-resolution SNP data now offer improved resolution. Here, we analyzed genome-wide SNPs from 71 Taiwanese Reeves’s muntjac and comparative Chinese samples. We detected deep divergence from Chinese muntjac (~0.24 MYA), and further north–south subdivision within Taiwan (~0.06 MYA). Demographic modeling revealed a complex history involving glacial isolation and asymmetric gene flow, mainly from north to south. Within Taiwan, genetic differentiation was shaped by both geography and climate, especially temperature annual range (Bio7), with niche models showing environmental separation. Selection scans identified PLA2-associated genes, potentially linked to thermal adaptation. This is the first study to demonstrate that both geographic and environmental heterogeneity jointly contribute to mammalian divergence in Taiwan. The repeated north–south split across ecologically diverse species highlights shared climatic and topographic factors driving parallel population structure in Taiwan’s montane ecosystems.