Oysters are globally recognized for their roles in improving water quality and building coastal habitat. However, due to overfishing and a long legacy of pollution, their populations in NY Harbor comprise less than 0.01% of their historical numbers (McCann 2019). In NY Harbor, the Billion Oyster Project (BOP) has restored small community oyster reefs at multiple locations, with variable success, which may be in part be due to shifting microbiomes under climate change and anthropogenic influence. In this project, we developed an oyster bacterial pathogen-monitoring tool that applies a novel generation of sequencing technologies to accurately identify bacterial pathogens at the species and subspecies level. The tool was developed specifically for use in monitoring of the eastern oyster in NY Harbor, but is modular and able to be implemented as a monitoring tool in other ecosystems or for other marine animal targets. In an initial proof-of-concept screening, we found over 1700 bacterial species across 10 NY Harbor oyster microbiomes. The most diverse microbiome contained a variety of probiotic and beneficial species while one of the least diverse seemed to be co-infected with several known marine bacterial pathogens.