The Nigerian indigenous pigs (NIP) are threatened to lose their genetic diversity through unsustainable farming practices in Nigeria. Therefore, the genetic relationships of NIP and commercially developed cross-bred pigs were evaluated to pinpoint a possible source of pure uncontaminated genetic stocks of NIP for conservation. Blood protein polymorphisms were used as a preliminary genetic analysis of blood samples from a total of 120 pigs (79 NIP from three separate locations and 41 cross-bred pigs). Nineteen polymorphic bands of the blood proteins globulin, transferrin and albumin were observed by sodium dodecyl sulphate-polyacrylamide gel electrophoresis (SDS-PAGE) and a phylogenetic dendrogram was developed to analyse the genetic relationship between the NIPs. The three NIPs were found to have a high genetic similarity (84 percent similarity coefficient), and were found to be distinctly different from the commercially cross-bred strains. One line from a farm in Ogbooro, Saki Oyo, Nigeria was identified as a relatively stable genetic resource that may be a suitable NIP for future conservation efforts.