This repository contains protocols used by the California Cooperative Oceanic Fisheries Investigations (CalCOFI) and Scripps Institution of Oceanography for collecting, processing, and analyzing eDNA and other Omics samples. These protocols are consistent with Better Biomolecular Ocean Practices (BeBOP) format including Minimum Information for an Omics Protocol (MIOP) and FAIR eDNA (FAIRe) terms.