In recent years, with the emergence and development of the high-throughput next generation sequencing technology, the cost of sequencing decreases continuously and the number of fungal species with complete genome sequence increases rapidly. Population genomics based on large-scale sequencing has also been gradually used in dissecting population structure, speciation, population divergence and locus-specific effects in fungi. In this review, we summarize the progress of population genomics in industrial fungi, pathogenic fungi, edible fungi, symbiotic fungi and genetic architecture dissection of phenotypic traits, and discuss future development.