To explore the phylogeography of Rattus tanezumi and Rattus norvegicus in China, 486 individuals collected from 31 localities were initially analyzed with mitochondrial DNA and 10 microsatellite loci. Then, 123 individuals from 18 localities were subjected to 2b-RAD analyses. There were several major findings. Although R. norvegicus is widely distributed in China, R. tanezumi is mainly distributed in southern China, but is currently invading northward and has occupied many regions of northern China. Development of shipping transportation in ancient China had an important role in expansion of these two species; except for westward and southward colonization by land, some individuals of R. norvegicus reached the southeast coast of China by shipping transportation and subsequently expanded to central China; R. tanezumi immigrated to the southeast coast of China from Southeast Asia, and then expanded to central and western China. Before large-scale expansion associated with human transportation, changes in Ne of these species were closely related to climate changes. However, after immigration of R. tanezumi into China, interspecies’ competition may have had a great role in their population sizes, as the R. norvegicus population declined rapidly with the increase of Ne for R. tanezumi. Analyses with 2b-RAD sequences did not support interspecies hybridization, although microsatellite data indicated potential gene introgression. Our study provided a valuable framework for further investigations on the expansion of the two dominant rat species in China. Finally, results also indicated that previous investigations on hybridization based solely on microsatellite data should be verified with genomic SNP data.