Human genetic diversity refers to genomic variation among races, ethnic groups, isolated populations and individuals worldwide, and is one major resource and tool on discovering human evolution and migration, interaction between genetic background and environment, and factors associated with human diseases and health. China has abundant and valuable resource of human genetic diversity due to 56 ethnic groups and a large population accounting for one fifth of the total population in the world. After decades of efforts, a large number of research data on human genetic diversity have been accumulated in China, and some of outcomes reach advanced international level. This review mainly focuses on the recent progress and outcomes achieved in applying genetic markers including morphological markers, biochemical and immunological markers and DNA markers in research of genetic diversity, and the application of mitochondrial DNA, Y chromosomal DNA, HLA and others in research of the origin and relationship of Chinese ethic groups, and the origin and mi-of modern East Asian populations. This review also summarizes the advances in the research fields of preservation and utilization of Chinese genetic resource, identification of genes associated with disease selective and adaptive for natural pressure, application of whole genome association study and next generation sequencing, and Chinese human genome as well.