Introgressive hybridization between mule deer (Odocoileus hemionus) and white‐tailed deer (O. virginianus) was studied using sequence analysis of the paternally inherited, Y‐linked, Zfy gene. The distribution of Zfy genotypes indicate that male white‐tailed deer disperse into the range of mule deer and successfully breed with mule deer does. In western Texas, F₁ hybrids are rare, but a relatively high proportion of backcross individuals was observed. Phylogenetic analysis of Zfy among white‐tailed, mule, and black‐tailed deer was consistent with traditional systematic placement of the latter two being sister‐taxa, whereas previous mtDNA studies suggested mule and white‐tailed deer were sister taxa.