Objective To investigate the 6 short tandem repeats (D2S1338,D8S1179,D16S539,D18S51,D19S433,D21S11) polymorphism in Maonan and Mulao minority and their genetic relationships with other 5 minorities in Guangxi Province and to enrich the genetic database of Maonan and Mulao populations. Methods The allelic frequencies and the genotype of six STR loci were generated from 383 unrelated Maonan and Mulao individuals by PCR-STR and ABI3100. Results Sixty-one and 65 STR alleles were found in the six STR loci of Maonan and Mulao populations, with their frequencies ranging from 0.002 5-0.320 0 and 0.002 7-0.284 2 respectively. Two hundred and sixteen and 218 genotypes were found in Maonan and Mulao populations,with their frequencies ranging from 0.005 0-0.150 0 and 0.005 5-0.158 5 respectively.Their average heterozygosities were above 0.8; polymorphism information content were above 0.8 their accumulative discrimination power were over 0.999 999 98, and the probability of paternity exclusion were over 0.998 3.The results of genetic distance and phylogenetic tree showed that there were closest genetic relationship between Maonan and Mulao minorities,and farthest genetic relationship was existed between Shui and Yi minorities.Seven minorities were clustered to 2 groups on phylogenetic tree.Yi minority was clustered to one group,whereas the other 6 minorities(Maonan,Mulao,Hui,Miao,Shu and Jing nationalities) were clustered to the other group. Conclusion Six STR loci of Maonan and Mulao minorities possesse the characteristic of high genetic diversities which has great practical value.Therefore,the obtained data can be used in human population genetics investigation,individual indentification and paternity test.The genetic variation of STR among 7 populations is basically consistent with their historical culture and geographic distribution.