There are eight distinct chromosomal races of the New Zealand weta Hemideina thoracica. We used mtDNA sequence data to test the hypothesis that these races originated on islands during the early Pliocene (7–4 million years ago). Nine major mitochondrial lineages were identified from 65 cytochrome oxidase I sequences. Phylogenetic analysis of these lineages suggests that they arose at approximately the same time. The geographical distribution of some lineages coincides with areas that were islands during the Pliocene. Overall, hierarchical AMOVA analysis shows that chromosomal races and Pliocene islands describe only 28% and 24%, respectively, of the total current mtDNA variation. However, removing one widespread (A) and one putatively introgressed (F) lineage increases these estimates to 65% and 80%, respectively. Intraspecific sequence divergence was very high, reaching a maximum of 9.5% (uncorrected distance) and GC content was high compared to other insect mtDNA sequences. Average corrected distance among mtDNA lineages supports the Pliocene origins of this level of genetic diversity. In the southern part of the species range there is reduced mtDNA variation, probably related to local extinction of H. thoracica populations from recent volcanic activity and subsequent re-colonization from a leading edge. In contrast, in this southern part there are five chromosome races, suggesting that chromosome races here may be younger than those in the north.