At a time when environmental degradation is outpacing efforts to survey extant biodiversity, environmental DNA (eDNA) sequencing offers a powerful application for biomonitoring. Given the potential to identify organisms throughout the Tree of Life, the addition of environmental DNA (eDNA) monitoring systems as a complement to traditional field surveys is anticipated to form a vital cornerstone of a comprehensive marine ecosystem observation network. As part of the Deepwater Horizon oil spill Natural Resource Damage Assessment Mesophotic and Deep Benthic Communities (MDBC) Coral Propagation and Habitat Assessment and Evaluation projects, eDNA samples were taken at nine mesophotic reef sites in the Pinnacles Trend and DeSoto Rim areas to complement and inform restoration investments for coral communities in the northern Gulf of Mexico (GOM) and provide the necessary baseline characterization to disentangle natural versus human-impacted seasonal shifts in biodiversity.