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In an era of rapidly changing habitat conditions, integrating conservation genetics and management to maximize the adaptive capabilities of rare species is paramount to their survival. We examine the genetic diversity and reproductive strategies of a rare wildflower endemic to the Florida panhandle, the Florida skullcap (Scutellaria floridana), to inform management and recovery decisions. We revisited almost all populations still considered extant and assessed genetic diversity and prevalence of clonal reproduction using SNP data generated by ddRAD sequencing. We found that populations possess low genetic diversity, moderate evidence of inbreeding, and moderate divergence from one another. We identified eight populations as possessing the majority of diversity within S. floridana’s gene pool and four populations of poor genetic diversity in need of further investigation. We established two plots to investigate asexual reproduction and identified only 2-3 genets out of 25 to 30 ramets in each. We suspect that five populations that we were unable to locate are extirpated and recommend further investigation to determine their status. Scutellaria floridana appears to have experienced a continued decline in the number of extant populations since its listing under the Endangered Species Act and will likely require ongoing monitoring and management to ensure its survival.