Studies on genetic diversity, as the core of population genetics, reveal genetic variations of the yak (Bos grunniens). Since the 1970s, the morphological, chromosomal, physiological, and biochemical characteristics, as well as DNA sequence polymorphisms, in yak have been extensively investigated. Following the rapid development of molecular genetics and DNA sequencing technology, the molecular genetic diversity of yak has become a focus in recent studies. In this paper, the research progress on the molecular genetic diversity of yak was reviewed based on the information and knowledge on mtDNA sequences and nucleus molecular markers, as well as candidate genes, obtained over the last 15 years. The future perspectives of relevant research topics were discussed to shed more light on depth understanding of the population genomics of the yak.