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The Hausa, Yoruba, Igbo and Fulani are arguably the first to fourth largest ethnic groups of Nigeria respectively. Forensic genotyping of Short Tandem Repeats (STRs) are used in creation of Combined DNA Index System (CODIS) databases and in evaluation of ancestral relationships between ethnic groups. This study computed Alleles Frequencies and phylogenetics of autosomal STRs in Fulanis and Yorubas resident in Ilorin, Kwara State and North-Central of Nigeria, and further compared the results with computed Alleles Frequencies of ethnic groups within and outside Nigeria and Africa. Samples of unrelated 25 Fulani males and 23 Yoruba males whose ethnicity were confirmed by three generations (paternal and maternal) were collected with informed consent. The samples were amplified using SureID®-21G PCR Amplification Kit containing Amelogenin and 20 autosomal STR loci: CSF1PO, D1S1656, D12S11, D12S391, D13S317, D16S539, D18S51, D19S433, D2S1338, D3S1358, D5S818, D6S1043, D7S820, D8S1179, FGA, PENTA D, PENTA E, TH01, TPOX and vWA; and genotyped subsequent to capillary electrophoresis. Phylogenetics analyses of Alleles Frequencies suggested that Hausas, Igbos and Yorubas are closely related, and are externally related to Guinea. Furthermore, neither Hausa nor Yoruba ethnic group is closely related to Egypt or Saudi-Arabia, and Igbos are not closely related to Israeli-Jews.