A total of 200 goats from three breeds namely Sahel (60), Red Sokoto (60), West-African Dwarf (60) and one strain; Kano Brown (20) were used to determine the phenotypic variation and Genetic diversity of Nigerian Indigenous goats. Morphological measurements were taken using a measuring tape in centimeters, they included; back length, height at withers and chest girth. Studies were also undertaken to determine the genetic diversity of Nigerian indigenous goats. Tissue samples were taken from the ears of 200 goats, 60 each from Sahel, Red Sokoto and West African Dwarf, while 20 were taken for the Kano Brown goat. DNA was extracted from the tissue using the Pure-link DNA kit and was genotyped using 25 microsatellite markers. The results of the morphological measurements indicated an average back length of 65.40 cm, 61.58 cm, 59.90 cm and 52.97 cm in Sahel, Red Sokoto, Kano Brown and West African Dwarf goats respectively, while the average heights at withers were 63.17 cm, 61.25 cm, 59.20 cm and 55.88 cm in Sahel, Red Sokoto, Kano Brown and West African Dwarf goats respectively. An average of 65.42 cm, 63.27 cm, 62.65 cm and 55.87 cm was obtained for chest girth in Sahel, Red Sokoto, Kano Brown and West African Dwarf goats respectively. Phenotypic correlations among the measured traits were positive and highly significant (P< 0.05) in most cases, ranging from 0.843 to 0.904, 0.671 to 0.737 and 0.626 to 0.728 for Sahel, Red Sokoto and West African Dwarf goats respectively. For the Kano Brown strain the correlations were not significant (P > 0.05) and ranged from 0.237 to 0.383. Out of the 25 micro-satellite markers, 23 were observed to be highly informative and polymorphic with the number of alleles ranging from 3 to 19. The highest observed heterozygosity was found in West African Dwarf and Kano Brown goats and the minimum in Sahel goat. In the entire goat populations, low inbreeding was observed (Mean inbreeding coefficient (Fis) was 0.105 and total inbreeding coefficient (Fit) was 0.129). The mean genetic differentiation (Fst) was 0.030 and demonstrated that about 96% of the total genetic variation was due to the genetic differentiation within individuals in each breed, while 4% was due to differences between breeds. The Red Sokoto and the Kano Brown breeds showed higher genetic similarity as observed in the genetic distance (0.022). High gene flow (Nm) was observed between Red Sokoto and Kano Brown breeds (13.59), similarly a high gene flow of 14.868 was observed across the studied goat populations. Significant deviations from the Hardy-Weinberg equilibrium were observed in all the populations. The phylogenetic tree and population structure displayed a remarkable degree of consistency with the goat’s geographical origins in the country while the population structure showed that the Nigerian goats are admixed possibly due to indiscriminate mating and high gene flow. From the results obtained, inbreeding and genetic differentiation among the studied populations was low whereas gene flow was high. Measures to conserve distinctiveness and uniqueness of indigenous breeds such as ex-situ and in-situ conservation should be carried out in Nigeria. Gene flow between populations should be controlled by adopting improved breeding and management practices.