The identification of sponges that lack a mineral skeleton is always highly challenging, especially for Hexadella species, which are also fibreless. Recently, the yellow species Hexadella pruvoti Topsent was identified as a cryptic species complex while the pink coloured Hexadella racovitzai Topsent showed two highly divergent lineages. We performed a COI phylogenetic reconstruction using 27 new Mediterranean Hexadella samples in order to confirm the presence of divergent lineages within both shallow-water species. Specimens were described with an integrative approach combining morphological and cytological investigations, biochemical profiling and assessment of natural toxicity in order to identify diagnostic characters for each taxon. H. topsenti, sp. nov. is distinguished from H. racovitzai by its colour, its surface network shape, divergent secondary metabolite patterns and toxicity values. H. crypta, sp. nov. differs from H. pruvoti by a different encrusting growth form when alive, and by distinctively colouring the ethanol fixative solution. In addition, H. pruvoti and H. crypta show different types of cells with inclusions as well as distinct metabolic fingerprints. Natural toxicity values, however, do not permit the separation of H. pruvoti and H. crypta. Our work shows that only the use of a combination of complementary tools can provide relevant descriptions for some problematic taxa.