In the eastern United States, there are nine species of subterranean termites in three genera: Reticulitermes (six species), Coptotermes (two species), and Prorhinotermes (one species). These species serve as important ecological players by decomposing cellulose material, and some are important structural pests. Many of these species are difficult to discriminate morphologically and require examining the reproductive or soldier castes, which can be difficult to collect. While some genetic tools have been developed for species identification, they are often expensive and time-consuming. To help facilitate identification, we developed a more cost-effective and rapid genetic method to identify Reticulitermes species by screening 10 PCR primers that amplified inter-simple sequence repeats (ISSRs) in other termite species. From these, one primer was amplified in all five focal Reticulitermes species and contained conserved, species-specific fragments. We further screened this identification method on samples of each species covering a diversity of mitochondrial DNA haplotypes and localities. This identification method utilizing ISSRs can be used to quickly identify five species of Reticulitermes subterranean termites in the eastern United States in a matter of hours, providing a useful technique for pest management as well as future ecological research.