Using morphological and molecular techniques we examined the corophiid amphipods in the Waimapu Estuary, Tauranga Harbour in the North Island of New Zealand. Based on morphology we identified two New Zealand endemic species, Paracorophium lucasi and P. excavatum, as well as P. brisbanensis, previously recorded only from the eastern coast of Australia and Corophium sp. which has not been previously recorded from New Zealand. Allozyme analyses confirmed the morphological diagnoses of three distinct species within Paracorophium and of the single Corophium species. The presence of reproductive females and juvenile P. brisbanensis suggests a viable, breeding population in Tauranga Harbour. We conclude that the species is likely to have been introduced to New Zealand waters via shipping activities (e.g., ballast water). The possibility that P. brisbanensis may now spread to other New Zealand ports as well as the consequences of this introduction for other New Zealand taxa need to be urgently examined.