Molecular analyses have led to an increased knowledge of the number and distribution of morphologically cryptic species in the world’s oceans and, concomitantly, to the identification of non-indigenous species (NIS). Traditional taxonomy and accurate delimitation of species’ life histories and autecology lag far behind, however, even for the most widely distributed taxa, such as the moon jellyfish Aurelia (Cnidaria, Scyphozoa) species complex. Here we analysed mitochondrial cytochrome c oxidase subunit I (COI) and nuclear 28S ribosomal RNA (28S) gene sequences to assign polyps, ephyrae, and medusae collected in the Mediterranean Sea to different phylogenetic species. We find evidence for three Aurelia species, none of which are referable to the type species of the genus, Aurelia aurita (Linnaeus, 1758), and describe the anatomical, morphometric, and developmental variation within and between them. We identify Aurelia coerulea von Lendenfeld, 1884 and Aurelia solida Browne, 1905 as established non-indigenous species in the Mediterranean Sea. We describe Aurelia relicta sp. nov., an endemic species currently unique to a population in the marine lake of Mljet (Croatia). These results demonstrate the usefulness of integrative approaches in resolving taxonomic uncertainty surrounding cryptic species complexes, identifying patterns of marine biodiversity, and recognizing non-indigenous species in marine ecosystems.