The black coral Leiopathes glaberrima is a foundation species of deep-sea benthic communities but little is known of the longevity of its larvae and the timing of spawning because it inhabits environments deeper than 50 m that are logistically challenging to observe. Here, the potential connectivity of L. glaberrima in the northern Gulf of Mexico was investigated using a genetic and a physical dispersal model. The genetic analysis focused on data collected at four sites distributed to the east and west of Mississippi Canyon, provided information integrated over many (~10,000) generations and revealed low but detectable realized connectivity. The physical dispersal model simulated the circulation in the northern Gulf at a 1km horizontal resolution with transport-tracking capabilities; virtual larvae were deployed 12 times over the course of 3 years and followed over intervals of 40 days. Connectivity between sites to the east and west of the canyon was hampered by the complex bathymetry, by differences in mean circulation to the east and west of the Mississippi Canyon, and by flow instabilities at scales of a few kilometers. Further, the interannual variability of the flow field surpassed seasonal changes. Together, these results suggest that a) dispersal among sites is limited, b) any recovery in the event of a large perturbation will depend on local larvae produced by surviving individuals, and c) a competency period longer than a month is required for the simulated potential connectivity to match the connectivity from multi-locus genetic data under the hypothesis that connectivity has not changed significantly over the past 10,000 generations.