Technical Abstract: For non-model organisms that do not have sequence information readily available AFLP is a well-established technique that can be used for genomic mapping applications such as genetic diversity studies or phylogenetic studies. While AFLP can be performed on a variety of systems including gel-based systems that require multiple labor-intensive steps, the availability of a more automated system that integrates the assay, electrophoresis platform and analysis software could enable researchers to greatly increase their throughput and facilitate routine AFLP analysis. We demonstrate the use of such a system for AFLP analysis on Hedysarum species. AFLP assays performed on samples belonging to two different species isolated from Utah identified different varieties that clustered as expected from their actual locations.