The Kokako (Callaeas cinerea) is an endangered, forest-dependent bird belonging to the endemic New Zealand family Callaeidae, the New Zealand wattlebirds. Two subspecies of Kokako are recognised: the now extinct orange-wattled South Island Kokako (SI Kokako) and the blue-wattled North Island Kokako (NI Kokako). The latter is the subject of intense conservation management and several populations have now been established on offshore island reserves. This study aimed to investigate the recent evolutionary history of Kokako through an assessment of the sequence variation and geographical distribution of mitochondrial haplotypes. We sequenced ~400 bases of the Domain III of the mitochondrial control region for 28 NI Kokako and two SI Kokako. Among NI Kokako, nucleotide diversity was low (0.006) but haplotype diversity was high (0.93). The average nucleotide diversity between NI Kokako and SI Kokako was 0.049 and a phylogenetic analysis revealed well supported reciprocal monophyly between NI Kokako and SI Kokako but no robust structure within NI Kokako. A nested clade analysis detected significant geographical structure in the distribution of the 13 NI Kokako haplotypes but could not identify an evolutionary scenario to explain the distribution. We discuss these findings in the context of the recent climatic and geological history of New Zealand.