Mitochondrial DNA (mtDNA) has been widely associated with complex traits in farm animals. The present study evaluated the effects of mtDNA on litter size in pigs. Mitogenome sequencing of 1017 sows distinguished 232 variations, including 229 single nucleotide polymorphisms and three indels, which constituted 11 haplotypes and further clustered into two haplogroups that differed significantly (P<0.05) in litter size. In order to explain the associations between the effect of haplogroup on litter size and different maternal origins, extant mitogenome sequences were used for phylogenetic or principal component analyses. The results of these analyses led to the identification of two groups, representing Chinese and European origins. The haplotypes corresponding to high litter size were all in the Chinese cluster, whereas haplotypes corresponding to low litter size were all in the European cluster. The results of this study suggest that the effect of haplogroup on litter size in the pig could be caused by diverse maternal origins, and that mtDNA haplogroup may be a marker for genetic selection for pig litter size.