Sequence analysis of the DNA fragments amplified with the DYS391, DYS437 and DYS438 primers allowed the detection of biallelic polymorphisms in the flanking region of these STR loci. In this work, we describe a methodology where both the STR alleles and the SNPs at these loci are typed. Sequencing of chimpanzee (Pan troglodytes) homologous loci was performed and the ancestral state of the SNPs was determined. The allele distribution of these biallelic markers was analysed within different haplogroups. For DYS391, allele 1 was found in all samples from haplogroups E3a and E* (xE3a). DYS437 allele 1 was present in all haplogroup E3a samples and absent in the haplogroup E* (xE3a). The presence of allele 1 of DYS438 was restricted to haplogroup J. The SNP typing can be helpful in distinguishing STR haplotype identity by descent from identity by state, thus proving to be very informative in forensic investigations.