Marine invertebrates produce a considerable number of structurally unique and biologically active compounds, also called secondary metabolites. The ecological roles of these natural products, although not completely understood, range from chemical defense against predation to intra-specific cues for larval settlement. Since the late 1960’s marine natural product bioprospecting has demonstrated that most of these molecules may be drug candidates. In addition to their pharmaceutical applications, secondary metabolites may also be employed as chemotaxonomic markers useful for elucidating classification problems and phylogenetic relationships. Drug discovery and chemotaxonomy are two main tracks in marine natural products chemistry which have attracted the attention of numerous biologists and chemists throughout the world. However, despite this intense global interest, the natural products chemistry of marine fauna of the western Indian Ocean islands is still largely ignored. This communication will therefore provide an outline of the contribution made by the Chemistry Laboratory of Natural Substances and Food Sciences (LCSNSA) at Reunion Island University to marine natural products research in the west part of Indian Ocean. During the last decade, our research program was concentrated on marine invertebrates from Madagascar and Mayotte, both showing an exceptional biodiversity. Among the numerous marine invertebrates encountered in these areas, sponges have predominated in all our collection expeditions and have therefore received special attention from our research group. Thus, in this communication, we wish to use our investigation mainly focused on sponge extracts from Madagascar and Mayotte to illustrate the two approaches of marine natural products chemistry: (1)New drug research with our investigation on secondary metabolites from the sponges Luffariella variabilis and Fascaplysinopsis sp.. (2)Chemotaxonomic study with our investigation on sterols from the sponge Petrosia spheroida.