The northern quoll (Dasyurus hallucatus) is the largest marsupial predator in the arid monsoonal tropics of northern Australia. This endangered species is believed to have undergone serious declines due to a multitude of factors, including habitat fragmentation, altered fire regimes, predation from feral cats, and more recently very high mortality due to poisoning from ingesting introduced cane toads (Rhinella marina). As a result, northern quolls have been the focus of intense conservation efforts to mitigate the impact of toads. The four disjunct populations of northern quolls are not currently recognised as taxonomically distinct, but they were originally split into four subspecies; D. h. exilis (Kimberley, WA) D. h. hallucatus (NT), D. h. nesaeus (Groote Eylandt, NT) and D. h. predator (Qld). There is mounting molecular evidence to suggest that northern quoll populations are clearly structured and exhibit deep divergences that most likely predate post-European range contractions. The most genetically distinct population is the Pilbara, which was not included in the original subspecies description as no specimens were available at the time. Here we examine a suite of qualitative morphological characters of the skull and skins of specimens from each of the four northern quoll populations. Using a statistical approach we investigate the distinctiveness of each population and if they should be recognised as separate subspecies. Using previously published molecular data and our morphological data we discuss possible divergence dates for each population and the potential geographic origin of this species, as well as conservation implications.