Phylogenetic analyses of three (3) local goat (Capra aegagrus hircus) breeds in Calabar was carried out. This involved the isolation and extraction of DNA from twenty one (21) blood samples collected from the 3 goat breeds - Red Sokoto (RS), Sahel White (SW) and West African Dwarf (WAD). The extracted DNA was amplified using PCR and separated in gel electrophoresis and subsequently, the gel was visualized using a UV trans-illuminator. Relatedness, genetic similarities and dissimilarities among the three goat breeds were determined using Darwin 5.0 computer software. Result showed that Red Sokoto species are genetically more distant from the WAD goat breed. The PCR amplified mtDNA loop from the 21 blood samples revealed that the ISSR primer amplified the selected genes obtained from all the blood samples. The highest number of samples were obtained from the RS breed which also showed 50% polymorphism. The evolutionary relationship among the goats sampled showed two major clusters. Cluster 1 consisted of all the RS goats and two (2) of the SW species. Cluster 2 consisted of all the WAD goats and two of the SW goats. ISSR primers proved to be efficient in determining the genetic similarities, dissimilarities and evolutionary relatedness among the goat populations. Further investigations on the relationship between these goat breeds should be carried out towards conservation and for future breeding purposes.

Keywords: Phylogenetic Tree, Dendrogram, Genetic distance, Polymerase chain reaction.

Abbreviations: Red Sokoto (RS); Sahel White (SW) ; West African Dwarf (WAD); Mitochondrial DNA (mt DNA); Inter Simple Sequence Repeat(ISSR)