This study examined genetic variations among indigenous and commercial pigs in Southwestern Nigeria. Sixty (60) individuals including Nigerian indigenous pigs (NIP) (n = 25), exotic (n = 25), and crosses between the exotic pigs (n = 10) were genotyped based on eight microsatellite markers. The mean number of alleles (Na) observed in the overall population of the three populations was 3.63 ± 0.36. Allele frequency ranged from 0.00 to 1.00 from the 39 alleles obtained within the population. Other allele frequency results obtained from the interpretation for the microsatellite loci across the three populations were polymorphic except for S0101 that was monomorphic. The mean number of effective allele (Ne) was 2.22 ± 0.17. The means obtained in this study for heterozygosities (Ho and He) were 0.529 and 0.501 respectively and the F-statistics showed the reduction in heterozygosity at various loci across the population studied i.e FIS and FIT. The mean values for FIS and FIT were − 0.06 ± 0.08 and − 0.02 ± 0.08, respectively. The mean level of gene flow (Nm) among the population was estimated to be 9.18 ± 3.59. The pairwise FST values among the three populations ranged from 0.02 to 0.04. The very low genetic differentiation between NIP and other populations reflects high gene flow. Molecular variance analysis revealed that there were 2% variance among the populations, 48% among the individual and 51% within the populations, with estimated variance of 0.04, 1.24 and 1.31 respectively. The phylogenetic tree separated the NIP from the remaining two populations while the exotic and the crosses clustered closely. This study revealed that genomes of pure indigenous pigs in Southwestern Nigeria are threatened by genetic erosion and recommend quick actions for sustainable conservation strategies.