Larval settlement is a vital transition period for marine invertebrates and can have far-reaching effects on the ecology and evolution of a species. To explore the molecular mechanisms of this critical process in a nonmodel organism, the abalone Haliotis asinina, we employed cDNA microarrays. By comparing gene expression profiles through mid- to late larval development and metamorphosis, we identified 144 genes as candidates for a role in competence and/or metamorphosis. Gene characterization indicates ~60% of these are significantly similar to known genes from other taxa, while ~40% are novel. A high 49.3% of genes are gastropod or abalone specific, but none appears to be Lophotrochozoan specific, even though metamorphosis is thought to have had a separate origin in this group. Differentially expressed larval and postlarval genes can be clustered into five categories that reveal strikingly different temporal transcriptional patterns occurring during this phase of development. Some gene activation is contingent upon exogenous cues and correlates with initiation of settlement. Importantly, there is also extensive gene activity associated with the endogenous attainment of competence, which occurs before, and independent of, the exogenous induction of settlement. Our results show that as the haliotid veliger larva matures, it requires coordinated regulation of temporally different batteries of genes involved in a wide range of physiological and developmental processes associated with benthic colonization. Although the signalling pathways operating at metamorphosis may be conserved across the animal kingdom, it appears they regulate the expression of novel genes specific to abalone, gastropods and molluscs during H. asinina metamorphosis.