Background: The maternally inherited mitochondrial genome encodes key proteins of the electron transfer chain, which produces the vast majority of cellular ATP. Mitochondrial DNA (mtDNA) present in the mature oocyte acts as a template for all mtDNA that is replicated during development to meet the specific energy requirements of each tissue. Individuals that share a maternal lineage cluster into groupings known as mtDNA haplotypes. MtDNA haplotypes confer advantages and disadvantages to an organism and this affects its phenotype. In livestock, certain mtDNA haplotypes are associated with improved milk and meat quality, whilst, other species, mtDNA haplotypes have shown increased longevity, growth and susceptibility to diseases. In this work, we have set out to determine whether mtDNA haplotypes influence reproductive capacity. This has been undertaken using a pig model. Results: To determine the genetic diversity of domestic pigs in Australia, we have sequenced the D-loop region of 368 pigs, and identified five mtDNA haplotypes (A to E). To assess reproductive capacity, we compared oocyte maturation, fertilization and development to blastocyst, and found that there were significant differences for maturation and fertilization amongst the haplotypes. We then determined that haplotypes C, D and E produced significantly larger litters. When we assessed the conversion of developmentally competent oocytes and their subsequent developmental stages to offspring, we found that haplotypes A and B had the lowest reproductive efficiencies. Amongst the mtDNA haplotypes, the number of mtDNA variants harbored at >25 % correlated with oocyte quality. MtDNA copy number for developmentally competent oocytes positively correlated with the level of the 16383delC variant. This variant is located in the conserved sequence box II, which is a regulatory region for mtDNA transcription and replication. Conclusions: We have identified five mtDNA haplotypes in Australian domestic pigs indicating that genetic diversity is restricted. We have also shown that there are differences in reproductive capacity amongst the mtDNA haplotypes. We conclude that mtDNA haplotypes affect pig reproductive capacity and can be used as a marker to complement current selection methods to identify productive pigs.