In pigs, genetic variability at the Cytochrome B (Cyt B) gene of mitochondrial DNA (mt DNA) has been widely used as a tool to determine genetic relationships between different breeds and population. The present study was carried out with the objectives to find out SNPs in Cyt B gene and decipher evolutionary relationship among the indigenous pigs based on it. Blood samples of 104 indigenous pigs viz.Ghungroo, Meghalaya local and Nagaland local, were collected and mt DNA was isolated. PCR-SSCP was carried out revealing monomorphic pattern comprising four similar bands. Representative samples of 3 different breeds were subsequently sequenced. Sequence analyses revealed presence of 4 SNPs at position 47(C), 49(A), 52(T) and 56(A) which corresponds to 15036, 15038, 15041 and 15045 nucleotide positions of mitochondrial genome, respectively. This particular combination of SNPs of CytB gene denoted Asiatic origin of indigenous pigs-further pointing to A1 haplotype.