Members of the genera Ctenopseustis and Planotortrix (Lepidoptera: Tortricidae) comprise 12 species of leafroller moths that are native to New Zealand. Females of this species complex produce a range of sex pheromones, typically blends of (Z)-5-tetradecenyl acetate, (Z)-7-tetradecenyl acetate, and (Z)-8-tetradecenyl acetate, that are unusual within the Tortricidae. To order the events in the evolution of this chemical communication system, 523 bp of the cytochrome oxidase I gene were sequenced in 16 taxa including all 12 species currently recognised within the Ctenopseustis and Planotortrix complex. 106 polymorphic sites were detected that included some intraspecific variation between host and pheromone races of C. obliquana. A maximum parsimony tree constructed from this data set supports many groupings previously determined using morphological and pheromone characters. These include such features as the monophyly of the genus Ctenopseustis, with C. servana as ancestral, and the existence of an excessana group that includes P. excessana, P. avicenniae, P. octo, and P. octoides. The few incongruent relationships derived from the different morphological, pheromone and molecular data sets are discussed. The phylogeny inferred from cytochrome oxidase I variation suggests an order for the evolution of the pheromones used by these species, including a number of independent gains and losses of the same pheromone component. For example, it appears that the ability to produce (Z)-5-tetradecenyl acetate has evolved twice within this complex.