Maguire primrose is a locally endemic plant of northern Utah, USA, with a total known range of less than 20 km2. A previous study found evidence for strong differentiation among local populations at 4 allozyme loci. Here we reexamined populations using 165 AFLP loci and found further evidence of unusually strong genetic structure. We also found an apparently fixed nucleotide difference between populations for a noncoding region of chloroplast DNA, mirroring the patterns seen for AFLP loci. Furthermore, we tested the hypothesis that the current population structure is the result of breeding barriers between plants from different populations. We made controlled hand-pollinated crosses and found that interpopulation crosses did not set significantly fewer seeds than intrapopulation crosses. Thus, we found no evidence of breeding barriers to explain these genetic patterns. However, we did note a relatively short overlap in flowering time, suggesting that phenology is a more feasible explanation for genetic differentiation than pollen-stigma incompatibility. Our study emphasizes that even locally endemic plants can house measurable genetic differences over a short geographic scale.