The distribution of Y-chromosome specific microsatellite DYS19, in 289 males of three ethnic populations in Hainan Island was studied with the method of PCR followed by denatured polyacrylamide gel electrophoresis and silver staining. The three ethnic populations are Bendi Li, Qi Li and Ha Li. The results showed that four alleles (190bp, 194bp, 198bp, 202bp designated as alleles B, C, D and E respectively), were observed in DYS19, the frequency ranged from 0.660-0.854, and was predominant in three Li subgroups. The pairwise comparison with Fisher's Exact test reveals that there exists significant difference (P<0.01) in DYS19 phenotype distribution between Qi Li and Ha Li populations. The polymorphism of the Y-chromosome specific Alu insert sequence DYS287 was investigated also in three Li populations. The results demonstrated that with 150 bp product in all Bendi-Li, Qi-li and Ha-li, YAP element is absent. The preliminary study provides reference populations for detecting male migration events and for reconstructing paternal history.