Abstract: Genetic diversity is one of the three dimensions of biodiversity and fundamental to various life forms on the Earth. Understanding the distribution pattern of genetic diversity and its driving forces has been an important topic in ecology, biogeography and conservation biology since the last decade. We investigated the genetic diversity pattern of passerine birds in the Mountains of Southwest China, a global biodiversity hotspot with the highest species richness of birds in the entire Eurasia, and explored the influencing forces of environmental variables on genetic diversity. We compiled 1189 Cytochrome b sequences of 27 passerine species from 152 geographic sites, covering the range of Mountains of Southwest China and its adjoining areas. We generated genetic diversity distribution maps using a grid-cell method based on nucleotide diversity and haplotype diversity indices. We further analyzed the variation pattern of the two indices along latitudinal, longitudinal, and elevational gradients. The correlations between the two indices and environmental variables were also evaluated. The nucleotide diversity hotspots were mostly located in the southern Hengduan Mountains, while for haplotype diversity, three hotspots were detected: the southeast edge of the Qinghai-Tibetan Plateau, the southern Hengduan Mountains and the Qinling Mountains. There was no monotonic increasing or decreasing pattern in nucleotide diversity or haplotype diversity along latitudinal, longitudinal or elevational gradients except for altitudinal range. Correlation and model selection analyses detected multiple environmental variables in driving genetic diversity patterns, including temperature, precipitation, vegetation, human influence, longitude and altitude range. Similar to the pattern of species richness, the nucleotide diversity pattern of passerine birds in the Mountains of Southwest China presents a decreasing trend from southwest to northeast, while the haplotype diversity pattern is more likely decreased from west to east. Our results indicate that the distribution pattern of genetic diversity may be derived from the complex topography and diverse microclimates in the Mountains of Southwest China.