Marine invertebrate larvae typically take hours to weeks after being released into the plankton before becoming “competent” to metamorphose. The mechanisms that govern this transition between the pre-competent and metamorphically competent states are unknown. We sequenced RNA from pre-competent and competent larvae of the salt-marsh dwelling polychaete worm Capitella teleta, a species in which pre-competent larvae are unusually easy to distinguish from competent larvae, to determine differences in gene expression associated with the onset of metamorphic competence.