Mitochondrial DNA (mtDNA) present in the metaphase II oocyte serves as a template for all mtDNA that is replicated during development and distributed amongst all tissues. In mammals, mtDNA is strictly maternally inherited and individuals with the same lineage cluster into groupings known as mtDNA haplotypes. In livestock, certain mtDNA haplotypes are associated with improved milk and meat quality, whilst other species have shown increased longevity, growth and susceptibility to diseases. In this work, we set out to determine the degree of mitochondrial genetic diversity within the Australian domestic pig population, and to find whether different maternal lineages influence reproductive capacity. Five mtDNA haplotypes (A to E) were identified from sequencing the D-loop region of 368 pigs. Whilst A, B and C were of Asian origin, D and E were of European origin. We then asked whether mtDNA haplotypes influence oocyte maturation, fertilization and development to blastocyst. We found that there were significant differences for maturation and fertilization rates amongst the haplotypes. Moreover, we found that haplotypes C, D and E produced significantly larger litters. To determine the relationship between mtDNA sequence variants and reproductive capacity, we performed next generation sequencing. 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 conserved sequence box II, which is a regulatory region for mtDNA transcription and replication. We conclude that the genetic diversity within Australian domestic pigs is restricted, and that mtDNA haplotypes affect reproductive capacity.