Quaternary climate change has accelerated species evolution. Periodic climate oscillations have driven the migration of different species between boreal and temperate areas, which has facilitated hybridisation between different taxa. Drastic climate fluctuations have isolated populations, which has imposed new selection pressures and potentially led to speciation. In this study, we integrated SNP and mtDNA data to investigate the complex reticular evolution history of four hare species, Lepus yarkandensis, L. tibetanus, L. tolai and L. timidus in northwest China, a biodiversity hotspot with diverse environments. Analysis of population structure and mito-nuclear discordance revealed extensive hybridisation among the four hare species. Phylogenetic analysis, population structure analysis, and F3 statistics revealed several genomic islands of differentiation between two genetically similar species, L. tolai and L. timidus, which may affect mate preferences. F3 statistics detected the gene flow between L. tibetanus and other hare species. Then the introgression regions were found by fd analysis, which may have influenced the adaptive evolution of L. tibetanus. Population history further indicated that the four hare species have experienced two severe bottleneck events. The first event was triggered by the Mid-Brunhes Event (MBE), which drove the migration of hares to limited refuges and possibly facilitated the emergence of L. tibetanus. The second event was likely caused by human activities, possibly due to the hunting of hares by early humans. Our findings provide new insights into the evolutionary history and speciation of Lepus in northwest China.