Species detection using environmental DNA (eDNA) is providing new capacity to monitor and characterize marine habitats, including deep-sea environments. The pelagic deep sea remains particularly challenging to investigate due to logistical constraints regarding access and collection of samples, making eDNA a promising tool for advancing our understanding of these ecosystems. However, incomplete reference libraries and the lack of vouchered specimens hamper the accuracy and reliability of eDNA-based studies. Here, we present collective efforts from the DEEPEND|RESTORE consortium to generate a regional mitogenome reference library for oceanic taxa and pelagic early life stages from the Gulf. Leveraging previous and ongoing sampling, we are sequencing, assembling, and annotating the mitogenomes of deep-pelagic fishes, crustaceans, and mollusks. All specimens were first identified by taxonomic experts, and sequenced specimens were vouchered in curated collections, ensuring traceability and long-term research value. This presentation will highlight current results of successfully assembled complete mitogenomes using a genome-skimming approach and discuss additional uses of the data beyond eDNA species detection. The resulting mitogenome reference database represents a valuable resource for researchers and management agencies seeking to monitor oceanic and pelagic early life stages of coastal taxa and implement eDNA as an additional tool in future analyses.