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Abstract Mollusks are an abundant group of animals, with many ecologically and economically important members that are phylogenetically distinct from nearly all genetic model organisms. This study provides a clade-wide evaluation of small RNA biogenesis pathways, with emphasis on the eastern oyster, Crassostrea virginica. A more thorough characterization of these molecules supports rationale design of RNA interference (RNAi) approaches for manipulation of mollusk genetics. Like other animal groups, mollusks have conserved microRNAs (miRNAs), with some shared with ecdysozoans and deuterostomes; however, there was no evidence of a dedicated endogenous small-interfering RNA (siRNA) pathway. These findings suggest that alternatives to long double-stranded RNA (dsRNA)-mediated knockdown, specifically short-hairpin RNAs or small duplex RNAs, are likely more appropriate for gene silencing in mollusks. The study also finds abundant Piwi-interacting RNAs (piRNAs) in both soma and gonads with some mollusk-specific aspects. Many invertebrates exhibit somatic piRNAs; however, mollusk piRNAs appear to be restricted to a subset of cells, suggesting that the potential of piRNA-based RNAi is also limited. Further, individual animals also express a unique collection of piRNAs that seem to be only partially determined through inheritance from parents. Together, this work defines the RNAi mechanisms in mollusks and provides insights into the phenotypic diversity seen in this group.