The horseshoe crab (Limulus polyphemus) is a valuable species environmentally, commercially, and biomedically. The population genetic health of horseshoe crab populations in South Carolina has been relatively unstudied. This project is a part of a greater ongoing study examining the genetic health of horseshoe crab populations along the southern coast of South Carolina. A suite of 11 microsatellites was used to analyze the Coffin Point and Harbor Island horseshoe crab spawning sites. Genetic structure was analyzed along with various genetic health metric tests. Results indicated the two sites represent a single population (Jost's D=0.0019, p=0.2679; FST=0.0058, p=0.2385). The population analyses showed moderately high diversity (HE= 0.762), no inbreeding (FIS= ‐0.0057), and a high Ne value based on the lower 95% confidence interval obtained from linkage disequilibrium‐based estimates of Ne (Ne > 2240.7). These are all positive indicators for the adaptive potential of the population. The results of this study serve as an important baseline for future conservation and management of horseshoe crab populations.