Prdm9 (PR domain containing 9) is the first hybrid sterility gene reported in vertebrates, it is a meiosis-specific gene and possibly related to male infertility. The objective of this study was to compare the Prdm9 zinc fingers of yaks (Bos grunniens, n = 33), Yellow cattle (Bos taurus, n = 6) and their sterile male hybrids (i.e., cattle-yaks, n = 7). Genomic DNA was extracted from muscle or testis tissues of the experimental animals, and PCR was performed to amplify zinc finger sequences of Prdm9. The PCR products were gel-purified and sequenced from both strands. The zinc finger sequence of yak Prdm9 is highly conserved, the deduced Prdm9 protein consists of 5 C₂H₂ type zinc fingers, which share identical sequences among 3 yak breeds or individuals. However, Yellow cattle Prdm9 showed variations in both sequence and numbers of zinc fingers among the 6 individuals, with zinc finger numbers of 5, 7 and 8 (5 in 4 cattle, 7 and 8 in 2 cattle). Amino acid sequence comparison of corresponding zinc fingers between yak and cattle revealed 6 polymorphisms and 9 mutations, and 7 of the mutations are located at the positive selection sites. These results indicate that the zinc fingers of Prdm9 gene evolves much faster in cattle than in yak. Further analysis of the zinc finger sequences of Prdm9 in sterile cattle-yaks showed that cattle-yaks carry heterozygous Prdm9 alleles, 4 of which contain alleles with different numbers of zinc fingers. Cattle-yak exhibits higher body size, milk and meat yields than those of yak, but F1 to F3 male sterility. We propose that the differences of Prdm9 zinc fingers at the positive selection sites as well as the numbers of zinc fingers between yak and cattle might be closely associated with the sterility of male cattle-yak.