The development of multicellular organisms from unicellular ancestors constitutes one of the major evolutionary transitions. At the molecular level, a key to organising and coordinating cells is the release of signalling molecules from one cell to stimulate another. From the study of peptide cell communication in basal metazoans, we can gain a better understanding of the fundamental signalling requirements that all animals need to function, regardless of complexity. Our focus was to initially define the peptide secretome of the marine sponge Amphimedon queenslandica. Secretory vesicles were isolated from adults and their protein contents analysed through mass spectrometry. Amongst those peptides identified included those with similarity to vascular endothelial factor and beta thymosin. These peptides have also been identified from secretome analysis of sponge adults and larvae. Secreted ependymin-like peptides within sponge cell aggregations were further investigated through production of a recombinant in a bacterial expression system; this is currently being analysed for structure determination which should provide some insight into its precise function, possibly in chemotaxis, cell proliferation or adhesion. The presence of lysine-arginine motifs in numerous precursor proteins, commonly used as cleavage sites within other metazoans, raised the possibility that A. queenslandica may have a similar secretory protein machinery. We identified 3 signal peptidase complexes, 5 prohormone convertases and 4 carboxypeptidases that are known to process and export secreted proteins and peptides. Some of these match closely with higher metazoan enzymes, while others are novel. The information gained from this research is expected to expand our knowledge in the area of cell communication and how multicellular animals established peptide communication.