Fat deposition in sheep tails has complicated mechanisms. In this study, the population genomics analysis has been applied to identify candidate genes associated with fat tails based on high depth whole-genome sequencing of Mongolia sheep (MG, fat-tailed), Small Tail Han sheep (STH, fat-tailed) and two dairy sheep breeds DairyMeade and East Friesian (DS, thin-tailed). The selective signature analysis demonstrated that GLIS1, LOC101117953, PDGFD and T were in the significant divergent regions between DS and STH-MG. A nonsynonymous point mutation (g. 27807636G>T) was found within GLIS1 in STH-MG and resulting in a Pro to Thr substitution. As a pro-adipogenic factor, GLIS1 may play critical roles in the mesodermal cell differentiation during sheep fetal development and affect the fat deposition in sheep tails. This study provides a new insight into the genetic basis of species-specific traits of fat tails.