As a result of high levels of historical commercial and recreational fishing, the Nassau grouper (Epinephelus striatus) has sustained widespread declines across its geographic distribution. Within US Virgin Islands waters, recognized spawning aggregations have declined to low levels; however, a remnant spawning aggregation historically numbering over 1000 individuals at Grammanik Bank, St. Thomas, has seemingly begun to recover since implementation of protective measures in 2005, and may now comprise approximately 200 individuals. The genetic consequences of such dramatic aggregation declines and incipient recovery are unknown. We report a preliminary genetic characterization of the St. Thomas aggregation using 14 microsatellite loci developed specifically for E. striatus, and address the hypothesis that the remnant population will show low genetic diversity and evidence of a genetic bottleneck. We genotyped aggregated individuals comprising three successive spawning years (2008, n = 54, 2009, n = 81; and 2010, n = 73). Analyses indicate relatively high current levels of genetic diversity (mean gene diversity = 0.805 and 0.814 and mean allelic richness = 11.01 and 10.93, for 2009 and 2010, respectively). Analysis of temporal collections is ongoing to monitor changes in genetic diversity as the aggregation recovers. Genetic analyses of 2009 and 2010 temporal samples using the software BOTTLENECK 1.2.02 provide mixed support for a genetic bottleneck. Future work will compare the genetic diversity status of the overfished St. Thomas aggregation to a relatively unfished aggregation inhabiting the waters off Little Cayman, Cayman Islands to further assess the genetic consequences of rapid and severe aggregation declines.