An intensive analysis was conducted of the maternal lineages of the Jeju native pigs (JNPs). A total of 100 mtDNA sequences from Asian wild boars (AWB), European wild boars (EWB), Asian domestic pigs (ADP), European domestic pigs (EDP), and JNPs were used for the phylogeny and network analyses. Two distinct JNP groups were found JNPA and JNPE in the Asian and European cluster. The maternal lineage of JNPE was the closest to that of EWB and a clear haplogroup sharing an identical haplotype (hap16) among 15 individuals of JNPE and 2 individuals of EWB was identified. However, except for hap18, no EDP shared any identical haplotypes with JNPE, suggesting that no obvious maternal contribution of EDP has occurred in JNPE in recent years. The possible existence of an additional and unknown path of maternal lineage from EDP into JNPE could therefore be postulated, in addition to those from AWB and ADP into the JNPA groups. Thus, JNPE appeared to have a pure maternal lineage that had no recent contact with EDP, and both the JNPA groups and JNPE are pure Jeju native pigs.