Despite exhaustive investigation of present-day Nautilus, the phylogenetic relationships of the five or six recognized species within this genus remain unclear. Mitochondrial and nuclear DNA sequence data plus a suite of morphological characters are used to investigate phylogenetic relationships. Systematic analysis of the morphological variation fails to characterize described species as independent lineages. However, DNA sequence analysis indicates that there are three geographically distinct clades consisting of western Pacific, eastern Australian/Papua-New Guinean, and western Australian/Indonesian forms. The morphologically and genetically distinct species Nautilus scrobiculatus falls outside the three geographically recognized assemblages. Members of the genus Nautilus also exhibit low levels of sequence divergence. All these data suggest that Nautilus is currently undergoing diversification, which may have begun only several million years ago. These data also suggest that some of the morphological features used to define Nautilus species may simply represent fixed variations in isolated populations within the same species.