Environmental DNA (eDNA), which is DNA left in the environment through the defecation or shedding of organic material (fur, skin, feces) from organisms, has proven to be an efficient and cost-effective tool in biomonitoring and biodiversity assessment in several ecosystems. Here used eDNA metabarcoding to survey wild populations of fish and shellfish such (e.g., longfin squid Doryteuthis pealeii, shortfin squid Illex illecebrosus, scallops, and sea urchins), in the Gulf of Maine (GOM) during the Maine’s Department of Marine Resources (DMR) inshore trawl surveys in spring and fall 2023. Specifically, we compared traditional trawl survey results to those from two eDNA collection methods: passive metaprobes attached to the codend of the trawl or by filtering slush water from the trawl. From eDNA samples we amplified fish, invertebrate, and cephalopod eDNA with general primers and sequenced the amplicons to infer species distribution. The goal of this study was to compare traditional trawl and eDNA surveys in terms of species composition and abundance of key shellfish species and determine whether and how eDNA surveys can be used to survey wild shellfish populations in the GOM. Results of this comparative study, as well as applications to aquaculture of cephalopods, bivalves, and urchins, will be discussed.