The adult and metacercaria life stages of a new species of the microphallid genus Atriophallophorus Deblock & Rosé, 1964 are described from specimens collected at Lake Alexandrina (South Island, New Zealand). In addition to molecular analyses of ribosomal and mitochondrial genes, metacercariae of Atriophallophorus winterbourni n. sp. from the snail host Potamopyrgus antipodarum (Gray) were grown in vitro to characterize internal and external morphology of adults using light and scanning electron microscopy and histological techniques. Atriophallophorus winterbourni n. sp. is readily distinguishable from Atriophallophorus coxiellae Smith, 1973 by having a different structure of the prostatic chamber, sub-circular and dorsal to genital atrium, rather than cylindrical, fibrous, elongate and placed between the seminal vesicle and the genital atrium. The new species is most similar to Atriophallophorus minutus (Price, 1934) with regards to the prostatic chamber and the morphometric data, but possesses elongate-oval testes and subtriangular ovary rather than oval and transversely oval in A. minutus. Phylogenetic analyses including sequence data for A. winterbourni n. sp. suggested a congeneric relationship of the new species to a hitherto undescribed metacercariae reported from Australia, both forming a strongly supported clade closely related to Microphallus and Levinseniella. In addition, we provide an amended diagnosis of Atriophallophorus to accommodate the new species and confirm the sinistral interruption of the outer rim of the ventral sucker caused by the protrusion of the dextral parietal atrial scale at the base of the phallus.