The taxonomic status of the lion’s mane jellyfish, Cyanea, of south-eastern Australia has been unsettled since 1884 when medusae from Port Jackson were described as a new variety of C. annaskala von Lendenfeld rather than assigned to C. rosea Quoy & Gaimard described previously from the same location. Cyanea annaskala was later combined with C. mullerianthe Haacke then synonymised with C. capillata (Linnaeus), which is now considered a circumglobal species, before being resurrected as a subspecies, C. capillata annaskala, in 1986. Here I demonstrate that Cyanea in southern New South Wales and Cyanea in Tasmania and Victoria constitute two distinct morphological groups separated by >10% sequence difference in both cytochrome c oxidase subunit I and internal transcribed spacer 1. Moreover, these clades are molecularly distinct (>6%) from C. capillata collected in its North Sea type locality. Analyses of medusae from another type locality, Port Philip Bay, Victoria, demonstrate that Cyanea annaskala von Lendenfeld is a valid species. Cyanea rosea is tentatively resurrected for medusae from New South Wales, pending confirmation by analyses of medusae from the vicinity of Sydney. Assigning other south-eastern Australian Cyanea specimens from museum collections to species is difficult in the absence of molecular analyses because biogeographic and morphological inferences sometimes conflict. Integrative molecular and morphological analyses of medusae from type localities may offer the most robust approach to straightening out the often convoluted systematics of scyphomedusae.