Twenty restriction endonucleases, ApaI, AvaI, BamHI, BclI, BglI, BglII, ClaI, EcoRI, EcoRV, HindIII, HpaI, KpnI, PstI, PvuII, SacI, SalI, ScaI, SmaI, XbaI, XhoI were used to investigate the mitochondrial DNA polymorphism of pigs from 11 localities in southwest China. Among the 28 animals analyzed, 27 restriction morphs were detected, which can be sorted into 6 haplotypes. The average genetic distance among haplotypes (P) is 0.004, and the value of average sequence variation in pig population (pi) is 0.122%. Our results suggest that the genetic diversity within the pigs is remarkably scarce. The pigs in southwest China may have origineted from a late common ancester, and were likely impacted by the founder effect.