Natural populations of marine invertebrates often exhibit measureable morphologic variation resulting in taxonomic confusion. This potentially has severe consequences for experimental design and data management. Species of the sponge genus Ianthella embody a number of different morphologies and a diverse range of secondary metabolites. Among them, Ianthella basta (Pallas, 1776), a common sponge in Papua New Guinea and the Great Barrier Reef (GBR), exhibits two dominant colour morphotypes: yellow and purple. Specimens collected from Orpheus Island on the GBR were investigated using phylogenetic (CO1, ITS-2 sequence analysis), chemical (mass spectrometry) and microbial (DGGE and 16S rRNA clone library) techniques in an effort to fully characterise the two colour morphs. Phylogenetic analyses indicated sharp genetic discontinuities within I. basta sensu lato independent of colour variation. The two morphotypes did, however, correspond to distinct DGGE profiles largely due to the presence of additional bands in the purple morpho-group. Further comparison of the microbial communities by 16S rRNA gene sequencing revealed that whilst both colour morphs were dominated by only two bacterial symbionts (residing within the Gamma and Alphaproteobacteria), the purple morph also contained minor representatives of the Cyanobacteria, Chloroflexi and Verrucomicrobia. Untargeted metabolic profiling by Fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS) indicated two distinct clusters corresponding to the different sponge colours. A clear association was found between the araplysillin class of compounds and the purple morphotype of I. basta, indicating the utility of a metabolomic approach to assess differences between colour morphs. These results have important implications for ecological investigations in sponges and other invertebrate taxa whose morphology is fundamentally dynamic, stressing the need for precise taxonomic, chemical and microbial descriptions.