Abstract: Today, the main threats for Sciurus vulgaris are illegal hunting, deforestation, and subsequent population fragmentation, combined with interspecific competition from S. carolinensis in some regions of Europe, which has led to a sharp reduction in the number of population. S. vulgaris has been listed as Near Threatened IUCN Red List and included in key protected wild animals in Jilin Province, China. The molecular ecology of S. vulgaris is developing rapidly with the rapid development of molecular biology methods. In particular, the research of mtDNA fragments and the application squirrel study microsatellite loci has further promoted the molecular ecology of S. vulgaris. In this study, the molecular phylogeny, the genetic diversity and the molecular phylogeography involving the molecular ecology of S. vulgaris were reviewed. Four areas for the future development in molecular ecology of S. vulgaris were proposed: 1) to further explore the molecular phylogeny relationship between S. vulgaris and S. lis; 2) the comparative analysis of the genetic diversity of S. vulgaris for continuous populations, isolated populations and metapopulation; 3) the analysis of molecular phylogeography of S. vulgaris based on other markers of nuclear; 4) to explore whether there existed the quaternary glacial refuge in Asia.