A combined molecular and morphological analysis was undertaken to resolve the systematics of the Miniopterus schreibersii complex in Australia. The study of skull morphology and sequence analysis of two mitochondrial genes, nicotinamine dehydrogenase subunit 2 and cytochrome-b, revealed three distinct Australian forms of M. schreibersii which are treated as subspecies. M. s. orianae occurs in northern Australia, M. s. oceanensis occurs in eastern Australia from Queensland through to central Victoria and M. s. bassanii, sp. nov. occurs in Western Victoria and eastern South Australia. The biogeographical history of the complex in Australia is discussed in the light of this new revision.