Abstract
The population genetic structure of the Canterbury mudfish (Neochanna burrowsius) (Phillipps), a threatened endemic freshwater fish of New Zealand, was investigated using DNA sequence data derived from the mitochondrial D‐loop region. Samples were obtained from eight sites throughout the Canterbury region of New Zealand. Comparison of 845 bp from the tRNA‐pro end of the D‐loop from the 79 fish sequenced revealed low genetic diversity. Only 13 (1.5%) of the 845 bp analysed were found to be variable and only nine unique haplotypes were revealed. DNA distance estimates and phylogenetic reconstruction of these haplotypes demonstrated that there is little divergence between populations. Despite this, the population structure was significant, with just one haplotype (9) detected at more than one site in the wild. This genetic structuring is attributed to recent dispersal from a small historical population and periodic bottlenecks within individual populations. DNA divergence estimates show a significant subdivision between northern and southern populations, indicating a historical separation. It is recommended that future conservation management priorities take into account this genetic structuring in order to adequately conserve the limited genetic diversity within this species.