The Atlantic blue crab [Callinectes sapidus (Rathbun, 1896)] is a commercially and recreationally important decapod crustacean found in estuarine and nearshore waters of the western Atlantic. Recent declines in abundance, compounded with a scarcity of biological and genetic information, have made blue crab a high-priority species for research and conservation in South Carolina (SC). A suite of microsatellite loci was used to estimate the genetic diversity and effective population size of blue crab collected from Charleston Harbor, SC, in 2012 to 2013. Genetic diversity of the Charleston Harbor blue crab population was relatively high, whereas inbreeding was fairly low. Effective size estimates were on the order of several hundred to several thousand individuals. The results of our study exhibit good indications for the overall genetic “health” of the Charleston Harbor blue crab population and provide valuable information that can be incorporated into management plans to aid in the conservation of blue crab in SC.