In an effort to improve cover crop performance, we have been breeding improved strains of the cover crop hairy vetch. Based on field data and molecular data, we realized that hairy vetch germplasm contains a genetically isolated subpopulation which can be reasonably considered a distinct species called smooth vetch (Vicia varia Host). These two species are visually quite similar, but have differences in agronomic performance (flowering time and winter survival). To provide a rapid, low cost method to screen individuals and determine their species, we collected single sequence repeat (SSR) marker data on a large number of individuals in the breeding program. Using individuals with known species identities from next-gen sequencing, we built a model to discriminate between the two species of vetch using a linear discriminant model. Properly identifying strains of cover crop vetch can improve agronomic outcomes and breeding progress.