Dietary DNA from the larval stages of two fishes, longfin smelt (Spirinchus thaleichthys) and Pacific herring (Clupea palasii) was sequenced targeting the mitochondrial cytochrome oxidase subunit I gene (COXI) using Illumina MiSeq high-throughput DNA sequencing. Concurrently collected environmental zooplankton samples were also sequenced to characterize the prey available to the larval fishes. Blocking primers were used to reduce the amplification of fish DNA in the sequenced samples. The samples are from the northern region of the San Francisco Estuary, San Francisco, CA, USA, primarily in February-June 2017.