Accurate identification of various life history stages and prey items of marine fishes and invertebrates is central for understanding distribution,abundance, trophic ecology, and biodiversity of these species. Taxonomic approaches have been successfully applied to ichthyoplankton identification and diet analysis efforts for many years. Identification to the species level requires varying degrees of taxonomic expertise. and diagnostic characters for eggs or larvae in some species have not been elucidated. In the current dataset we assembled a mitochondrial DNA (mtDNA) database for which used standard laboratory protocols (restriction fragment length polymorphism and Sanger DNA sequencing) to accurately identify any life history stages of selected fish and shrimp species, with special emphasis on those species that have been difficult or impossible to identify by conventional taxonomic means. Fish and shrimp specimens were collected between 2010 - 2013. We developed a restriction fragment length polymorphism (RFLP)protocol, based upon mitochondrial DNA sequences to distinguish between Pacific halibut and Greenland halibut, but were unable to develop one to discriminate between Bering flounder and flathead sole. We used direct Sanger sequencing of mitochondrial DNA for species identification of 32 species of sculpin and four species of caridean shrimp. PCR products from fish and shrimp samples were sequenced using an ABI 3730 automated sequencer (Applied Biosystems, Inc). DNA sequences from museum voucher specimens were compared with entries in the public databases for those species. Sequences from voucher specimens have greater taxonomic authority for use in species identification than those without vouchers, adding greater confidence to species identifications based upon our data.