This paper deals with two deep water coral ecosystems off the North Carolina coast, both under the depositional, erosional, and biological influence of the Gulf Stream and its eddies and episodic upwelling processes. The first coral community, Ben Franklin temperate reef, is located at 20 meters in Onslow Bay and is characterized by the ahermatypic coral Oculina arbuscula Verrill and unusually high abundance of the small predatory isopod Eurydice bowmani George and Longerbeam. The deep sea coral community, Agassiz Coral Hills, is located over the Blake Plateau at 650 meters, dominated by the fossilized, dead and living coral Bathypsammia tintinnabulum, with rare occurrence of the deep sea solitary coral Flabellum goodei. The deep sea coral sites were sampled with an otter trawl, outfitted with `Benthos' flotation spheres. The results suggest that the fish and shrimp fauna exhibits high species richness in the Agassiz Coral Hills off North Carolina in comparison with a control site over the Blake Plateau off Florida. Species richness may be linked to episodic upwelling events along the Gulf Stream meanders. The fish fauna in the Agassiz Coral Hills includes the following two commercially important deep sea fish species: the wreck fish Polyprion americanus and the eel Synaphobranchus koupi. The Ben Franklin reef and the Agassiz Coral Hills are recommended as Marine Protected Areas.