The critically endangered Capricorn yellow chat (CYC) is endemic to coastal central Queensland on marine plains where it occurs in three areas, numbering <300 birds. Recent industrial expansion in the region has increased the threat to the CYC. To assist management of the subspecies, a phylogeographical evaluation of the CYC using mitochondrial DNA was undertaken. We found no genetic diversity within, nor genetic divergence between, the two areas at the northern and southern extremes of their current distribution, and only slight morphological differences. These findings suggest that the two groups of CYC represent daughter populations of an ancestral population that was affected by a genetic bottleneck in the recent past. Implications for conservation of the subspecies could be increased vulnerability to environmental change. A preliminary evaluation of the divergence between the CYC and its nearest subspecies, the widespread inland yellow chat, indicate a time to the most recent common ancestor of 215 000 years or less. This timespan overlaps two periods of glacial aridity during which xeric habitats used by yellow chats for breeding, such as semiarid and arid swamps, may have expanded, allowing colonisation of the coastal marine plains. CYCs may represent a relictual population from a previously more xeric era that has subsequently become isolated as the region became wetter following glacial maxima.