The genus Conus has over 500 species and is the most species-rich taxon of marine invertebrates. Based on mitochondrial DNA, this study focuses on the phylogenetics of Conus, particularly the pennaceus complex collected along the Mozambican coast. Phylogenetic trees based on both the 16S and the 12S ribosomal genes grossly revealed the same groupings: one that clustered the individuals from the north (Pemba, Nacala and Island of Mozambique), another that grouped the individuals from the central/southern coast (Pomene/Massinga and Inhambane) and a third that assembled the specimens from the central/southern islands (Bazaruto and Inhaca). The 16SrRNA-based trees further distinguished the northern group into a Nacala group and a Pemba+Island of Mozambique group. In all trees, C. p. bazarutensis and C. lohri collected on the central/southern islands grouped separately from the C. p. bazarutensis and C. lohri collected on the central/southern coast, suggesting a genetic similarity between these species. Likewise, C. praelatus revealed greater proximity to C. pennaceus from Pemba. Although different topologies were produced by each gene (low bootstrap support in some nodes), we support the hypothesis of a southward ancestral colonisation pattern, indicated by the 16SrRNA trees. The common ancestor would have shifted from planktonic to non-planktonic larval development and this weak vagility would have promoted the divergence between north and south specimens. Our results suggest that the separation of these groups might have been a relatively recent event, and part of the current morphological variability could be the outcome of phenotypic plasticity and/or ecological adaptation.Keywords: complex, Conus pennaceus, mitochondrial genes, morphological diversity, MozambiqueAfrican Journal of Marine Science 2010, 32(3): 591–599