Abstract: To explore the paternal genetic differences between Huzhu white yaks in Qinghai Province and Tianzhu white yaks in Gansu Province, the genomic DNA from 32 Huzhu white yaks and 34 Tianzhu white yaks was amplified by PCR method, sequenced and genotyped by using five Y-SNPs（SRY4, USP9 Y, UTY19, AMELY3 and OFD1 Y10） and one Y-STR（INRA189） markers. The paternal genetic diversity, population structure, differentiation and genetic background of the two white yak breeds（populations） were comprehensively analyzed by using Bioedit 7.2.5, Arlequin 3.11, network 10.1 and other bioinformatics software. The results showed that five Y-haplotypes were identified totally in two white yak breeds（populations）. Among them, four Y-haplotypes（H1 Y1, H10 Y1, H11 Y2 and H12 Y2） were identified in Huzhu white yaks and five Y-haplotypes（H1 Y1, H10 Y1, H11 Y2, H12 Y2 and H13 Y2） were detected in Tianzhu white yaks. The Y-haplotype diversities of Huzhu white yaks and Tianzhu white yaks were 0.750 0±0.034 9 and 0.688 1±0.061 4, respectively. The fixed differentiation index value of the two white yak breeds（populations） was 0.018 6（P＞0.05）, which showed no significant difference（P＞0.05）. Both white yak breeds（population） were composed of two paternal lineages（haplogroups） of Y1 and Y2. The Y1 lineage（haplogroup）（59%） was dominant in Tianzhu white yaks, while the Y2 lineage（haplogroup）（56%） was dominant in Huzhu white yaks. In conclusion, both Tianzhu white yaks and Huzhu white yaks had rich paternal genetic diversity, but the level of paternal genetic diversity in Huzhu white yaks was slightly higher than that in Tianzhu white yaks. The paternal genetic differentiation between two white yak breeds（populations） was small. White yaks had two paternal origins. Both Tianzhu white yaks and Huzhu White yaks were composed of two paternal lineages（haplogroup） of Y1 and Y2, but Y1 and Y2 were the dominant lineages（haplogroup）, respectively, indicating that there were some differences in the paternal genetic structure.