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Carter's mustard (Warea carteri) is an endangered, fire‐stimulated annual endemic of the Lake Wales Ridge, Florida, USA. This species is characterized by seed banks and large fluctuations in plant numbers, with increases occurring in postdisturbance habitat. We investigated the mating system, patterns of isozyme variation, and effective population sizes of W. carteri to better understand its population biology and to comment on reserve designs and management proposals relevant to this species. Warea carteri is self‐compatible and autogamous, and probably largely selfing. Measures of genetic variation in W. carteri were lower than values reported for species with similar ecological and life history traits (6.6% of loci polymorphic within populations, 1.87 alleles per polymorphic locus, and 0.026 and 0.018 expected and observed heterozygosity, respectively). The high average value for Nei's genetic identity (0.989 …