DNA Finger Printing of three goat breeds Red Sokoto (RS), West African Dwarf (WAD) and Sahel White (SW) in Nigeria was carried out. Standard procedures for blood sample collection, DNA extraction and analyses were employed. Analyses carried out included PCR amplification, band scoring, Population Differentiation investigations and percentage variability studies. Results obtained revealed 58.33%, 100% and 50% amplifications of the RS, WAD and SW breeds respectively; band scoring revealed polymorphism across the goat breeds; population differentiation showed four population structures and percentage variability studies gave 100% variability within the goat breeds and 0% among breeds. These results indicate high genetic variability of the three goat breeds and presents the ISSR primer as an appropriate tool for diversity studies of these breeds.