Genetic introgression from Chatham Island Red-crowned parakeet (Cyanoramphus novaezelandiae chathamensis) is a long-standing problem in the conservation of the rare Forbes' parakeet (C. forbesi) on Mangere Island, New Zealand. Microsatellite genotypes, mitochondrial DNA sequences, and morphological markers have been applied to study the situation. An extensive history of hybridisation was detected in the single remaining Forbes' parakeet population, where no less than 81% of all birds screened are considered hybrids. Genetic markers showed that a large proportion of birds identified as Forbes' parakeets by crown plumage are cryptic hybrids. Only a small proportion of birds with Forbes' parakeet morphotype were found to be genetically distinct from Chatham Island Red-crowned parakeets using microsatellite and mitochondrial DNA assignment tests, but these still represent an Evolutionarily Significant Unit (ESU) for conservation.