Haplotype frequencies for 16 Y-chromosomal short tandem repeat (DYS456, DYS389I, DYS390, DYS389II, DYS458, DYS19, DYS385a/b, DYS393, DYS391, DYS439, DYS635, DYS392, Y GATA H4, DYS437, DYS438 and DYS448) loci, included in the AmpFLSTR Yfiler PCR Amplification Kit, were analysed in 110 Fang and 133 Bubi individuals from Bioko Island, Equatorial Guinea. The diversity was higher in Fang population, probably since they were originally from the mainland, with which they maintain tribal village and family links, and to which they travel frequently. Comparisons were made with previously published haplotype data on European and African populations, and significant differences were found between them.