Useful genetic diversity found in wild potato germplasm is important for progress in potato breeding and science. An effective way to maximize its utilization is through characterization of ex situ collections. For example, marker-based core subsets from large collections is an effective strategy to accelerate evaluation, utilize germplasm and, enhance cost-effectiveness. This project used AFLP markers to create a core subset for the US Potato Genebank’s collection of S. demissum. This Mexican species is known for excellent levels of late blight resistance and frost tolerance. A total of 149 accessions with diverse geographic origin were characterized with 1403 AFLP markers; these markers were effective on determining genetic associations among the accessions. For the core subset, the AFLP loci were considered as traits, with the presence of the marker as the required state to include in a core set. The results of the analyses identified that 10 of the accessions of demissum captured 83% of all the markers detected in the whole collection. The inclusion of 28 additional accessions, which had between 1 to 5 unique markers, resulted in a core set of 38 accessions that captured 96% of all the marker diversity. We expect this can benefit the genebank and the potato community by opening opportunities for promoting trait screenings and, marker association studies.