Evolutionary analysis of mating systems in broadcast-spawning marine animals and plants has focused on sperm- and egg-surface proteins and glycopeptides that mediate reproductive interactions at different stages of gamete recognition. Improved understanding of the ecology and evolution of such interactions depends on extending our knowledge to multiple genes expressed in both sperm and eggs of diverse taxonomic groups with different modes of fertilization. Here, we use readily accessible next-generation sequencing methods and desktop bioinformatics to characterize the repertoire of highly expressed genes in testes and ovaries of the asterinid sea star Patiria miniata, including gene ontology annotations for male- and female-expressed molecules, and descriptions of two genes that encode egg-surface molecules involved in fertilization that have not previously been studied in sea stars. The results are used to contrast expression differences between the testis and ovary, and to develop hypotheses of gamete-specific expression. We also explore differences in ovary gene expression among multiple females from northern and southern populations that show nucleotide differentiation at many non-expressed loci and at a gamete recognition locus.