Pennycress (Thlaspi arvense) is a winter annual plant species that has gained popularity as a winter cover crop and biofuel feedstock. Pennycress can be planted in the fall and grown over the winter, helping limit nutrient runoff and spring weed growth. In the spring, the oil-rich pennycress seed can be harvested in time for the planting a spring crop and used as a biodiesel feedstock. While current pennycress lines show promising agronomic properties, there has been little selective breeding for or improvement of traits such as: seed dormancy, speed of development, or oil content. The creation of a dense linkage map will aid in the development of a large-scale breeding program needed to achieve these goals. As a first step to develop this map, a draft genome for two lines of pennycress has been used to identify the putative locations of single nucleotide polymorphisms (SNPs). SNPs that overlay restriction enzyme sites (cleaved amplified polymorphic sequences (CAPS)) were used to test the accuracy of SNP calls. Future work will identify additional SNPs in multiple pennycress lines to aid in the breeding program.