Abstract The aim of this study is to characterise genetically the Annobon Island population to compare it with other ethnic groups from Equatorial Guinea. Annabón Island is volcanic, with an area of 17 km 2 and 5008 inhabitants (according to the 2001 census). Haplotype frequencies for 16 Y-chromosomal STR loci, included in the Y-Filer™ kit, were determined in 31 unrelated healthy males. Twenty-three different haplotypes of Y-chromosome were identified and 17 were unique. Haplotype diversity was 0.9785. Allele frequencies for 15 STR loci, included in the AmpF lSTR ® Identifiler™ kit, were analyzed in 69 unrelated healthy individuals. For all polymorphisms, the observed genotype frequencies are in good agreement with the expected distribution under Hardy–Weimberg law. From a forensic point of view the heterozygosity value, power of discrimination and the a priori chance exclusion value were calculated to be >0.9999, >0.9999 and 0.9999995, respectively. The population data obtained for these loci were compared with the Fang and Bubi population from Equatorial Guinea, previously published by our group.