Sixty-two pigs (32 large white pigs and 32 Nigerian indigenous pigs were used in this study. Biochemical techniques were used in analyzing the blood serum samples obtained from the pigs using Polyacrylamide Gel Electrophoresis. A total of 14 loci were scored for the Nigerian Indigenous pigs and 10 for the Large White breed. The results of the molecular characterization with SDS-PAGE were analysed using PAST Package to determine genetic similarity coefficient and construct phylogenetic dendrogram. The within breed comparism of Nigerian indigenous pigs showed 62% similarity while the Large White breeds showed 65% similarity. For the between-breed comparism, the Nigerian indigenous breeds and the Large White breeds were 48% similar. The moderate genetic similarity observed in the Nigerian indigenous pigs and the Large White pigs indicates a reasonable level of genetic dilution in both breeds.