Crocanthemum dumosum is a globally rare plant endemic to the northeastern United States. The species is considered vulnerable to extinction due to its limited range and low population numbers. This taxon is often confused with its wide spread relative C. canadense, and its recognition as a separate species is often questioned. Within the range of C. dumosum there are three other species that belong to the genus Crocanthemum. In this study, we used AFLP markers to evaluate genetic variations among populations of the four Crocanthemum species found in the southern New England region with special focus on the genetic relationship between C. dumosum and C. canadense. The AFLP data showed that the four Crocanthemum taxa in the southern New England region had high among population and low within population genetic diversity. UPGMA clustering and principle coordinate analysis clearly separated C. bicknellii and C. propinquum from each other and from C. dumosum and C.canadense, indicating significant differences in their genomes and further supporting their distinction as separate species. However, C. dumosum nested within the same cluster as C. canadense which suggest their genomes are very similar. Based on the results from our molecular data and that of the previous morphological analyses, we find insufficient evidence to support the distinctiveness of C. dumosum from C. canadense and we recommend that it be considered as a subspecific variant of C. canadense. Furthermore, we suggest that these findings be taken into consideration during review of C. dumosum conservation status.