Del Mar manzanita (Arctostaphylos glandulosa Eastw. subsp. crassifolia (Jeps.) P.V. Wells) is a federally listed endangered shrub found in San Diego County, California and Baja California, Mexico. This manzanita forms part of the imperiled southern maritime chaparral of southwestern California and adjacent Baja California, Mexico. Del Mar manzanita is problematic to identify because of morphological intergradation with other subspecies of A. glandulosa. Such intergradation could result from biological phenomena, such as gene flow among subspecies. Alternatively, it could be that the current circumscription of the Del Mar manzanita is not correct, and that the morphological characters used to diagnose this subspecies are inaccurate indicators of underlying genetics. This situation leads to problems for conservation planning, where accurate identification of individual plants is essential. Here, we used high-throughput sequencing of restriction-site associated DNA markers (RADseq) to develop single nucleotide polymorphism (SNP) data for a large sample of putative Del Mar manzanita, and a small sample of closely related subspecies of A. glandulosa. We analyzed genetic relationships using a total of 65,964 SNPs, with the aim of testing whether morphological traits used to identify Del Mar manzanita are an accurate reflection of underlying genetic patterns. We conclude that vegetative morphology is a poor predictor of genetic patterns, and that the current morphology-based circumscription of Del Mar manzanita is probably in need of some change. However, due to the limited sampling of A. glandulosa subspecies in this study, it is not possible to determine the taxonomic limits of Del Mar manzanita using our SNP data.