There is an interest to develop sugar kelp (Saccharina latissima) cultivation in the rural, eastern Maine region of the United States. Future farming efforts would benefit from an understanding of the genetic diversity and population structure of kelp to inform management and conservation, and to identify genetic resources. The purpose of the present study was to characterize the fine-scale population genetic structure of kelp in eastern Maine using 12 microsatellite loci. A total of 188 samples were genotyped from five sampling locations. Overall, kelp exhibited relatively low genetic diversity and small but significant differentiation among populations (FST = 0.0157). The greatest genetic difference was detected between two geographically close populations in Penobscot and Frenchman Bays, which is likely due to patterns in the Eastern Maine Coastal Current that may limit meiospore recruitment. The population structure could not be fully explained by an isolation-by-distance model. Fine-scale structuring was also detected among populations along the more continuous eastern Maine coastline. These differences highlight that sugar kelp populations are finely structured across small spatial scales, and that future management and farming efforts should aim to maintain genetic diversity and assess the culture potential of local populations.