Two regions of the mitochondrial genome (cytochrome oxidase I and ATPase 8–ATPase 6) were used to examine the population genetic structure of New Zealand’s endemic abalone (Haliotis iris). Samples were collected from 28 locations around New Zealand between January 2005 and February 2008. At least four phylogeographic breaks were present and occurred across the Chatham rise, in the western Cook Strait region, along the southeast coast of the South Island, and at East Cape in the North Island. Gene flow across the Chatham rise is probably limited due to infrequent dispersal across large geographic distances (~850 km), while factors limiting gene flow around the North and South Islands are less clear, and understanding these may require intense temporal and spatial sampling in complex hydrographic regions. High genetic diversity and weak genetic structure may be a general feature of abalone potentially reflecting large and/or ancient populations.