Population genetics is a valuable tool in understanding various aspects of biological invasions, such as pathways of invasions, predicting invasion success, and determining dispersal capabilities. The island apple snail (Pomacea maculata), which is native to South America, is an invasive gastropod currently established in several southeastern states in the United States, including South Carolina and Georgia. Despite its known negative impacts in invaded regions, knowledge of P. maculata specific to South Carolina is limited, and an in-depth analysis of the population genetic structure of P. maculata in South Carolina and Georgia has not been conducted. The present study aimed to genetically characterize P. maculata individuals from three locations in South Carolina and five locations in Georgia using a suite of 14 microsatellite markers. Population genetic structure was determined using pairwise FST comparisons, isolation by distance analysis, and a likelihood-based approach. Genetic diversity indices, effective population size, inbreeding coefficients, and Garza–Williamson indices, which is the mean ratio of number of alleles to the range in allele size in a population and can be used to detect recent reductions in population size, were all calculated. Significant genetic structure was observed in all sampling locations, apart from the two sites in Kingsland, GA; a weak correlation was found between genetic distance and geographic distance across all the sites; and genetic diversity was low across all loci at the eight sites. Garza–Williamson indices all showed likely recent reductions in population size. These results indicate that the populations in South Carolina and Georgia were probably the result of separate introduction events and that these populations are genetically isolated. The low genetic diversity observed could indicate that these populations are susceptible to eradication efforts and/or stochastic environmental changes.