Malays in Malaysia are a mixture of different races, caused by the history of migration centuries ago and may consist of 14 sub-ethnic groups. We used the Y-chromosomal STR (Y-STRs) to genotype two of the sub-ethnic groups namely, Kelantan and Minang Malays. In this ongoing study we investigated the polymorphisms of six YSTR loci namely, DYS19, DYS388, DYS390, DYS391, DYS392 and DYS393 in the two populations mentioned. Twenty males (10 Kelantanese and 10 Minang) were analyzed by PCR amplifications followed by 8% nondenatured polyacrylamide gel electrophoresis. Randomly selected samples were sequenced for validation. Results revealed a total of 32 alleles, ranging from three (DYS19) to nine (DYS390). Allele frequency distributions ranged from 0.05 (DYS388, DYS 391, and DYS393) to 0.65 (DYS388). Although the level of polymorphisms of the two sub-groups were similar (average number of alleles, 4; average heterozygosity, 0.6), allele frequency distribution appeared to be imbalanced. Significant differences of allele frequency distributions were observed in loci DYS390, DYS391, and DYS393. None of the individuals shared the same haplotypes. However, errors of scoring and factors like small sample size should be considered. Preliminary results revealed polymorphisms in the six loci among the two Malay sub-ethnic groups. Significant differences of the allele frequency distributions were observed, but a further investigation with a larger sample size is warranted to confirm these findings.