This study was conducted to determine the genetic relationships among and population history of four Ni-gerian indigenous goat populations. A total of 200 goats from three breeds namely Sahel (60), Red Sokoto (60), West-African dwarf (60) and Kano Brown, a strain (20), were used for the study. Tissue samples were collected from the ear of animals using an Allflex® ear punch tissue sample collector, and aliquoted into plastic tubes containing the Allflex® tissue preservative. DNA extraction, amplification and sequencing were carried out at the International Livestock Research Institute (ILRI), Nairobi, Kenya. Genetic analysis of the DNA was carried out using 25 microsatellite markers proposed by Food and Agricultural Organiza-tion and International Society for Animal Genetics (FAO-ISAG). From the results of the study, the highest heterozygosity was observed in Kano Brown goats (0. 68± 0. 04), which was followed by that of Red Sokoto goats (0. 64± 0. 04) and that of West African dwarf goat (0. 58± 0. 05) as the least. In the entire goat popula-tions, low inbreeding was observed; mean Fis was 0. 105 and Fit was 0. 129. As expected, populations of Red Sokoto and Kano Brown showed higher genetic similarity as was seen in the genetic distance (0. 022), con-firming the notion that the Kano Brown is a strain from the Red Sokoto breed. Gene flow (Nm) played an important role in the genetic uniformity in populations of narrow geographical vicinity (14. 868). The den-dogram displayed a remarkable degree of consistency with the geographical origin of goats in this country. The information obtained in this study will aid in rational development, utilization and conservation of Ni-gerian indigenous goats.