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Premise of the study: Although species adapted to grow in unusual soils contribute importantly to regional diversity, the microevolutionary processes responsible for that diversity remain to be understood. We aimed to answer this question by analyzing which processes are responsible for the genetic differentiation in Fouquieria shrevei (Fouquieriaceae), a species confined to gypsum soils of northern Mexico.

Methods: We analyzed sequence variation in three chloroplast intergenic spacers from five populations.

Key results: Total genetic diversity was high (H-d = 0.743). Genetic differentiation was high (F-ST = 0.651), as most haplotypes were unique to individual populations, and three populations had only one haplotype. Haplotypes were more similar in nearby populations, resulting in a phylogeographic structure (i. e., G(ST) = 0.850 was significantly lower than N-ST = 0.930) and a significant Mantel test (P = 0.04). Tajima’s D (-0.019, not significant) indicates that effective population size has remained constant.

Conclusions: We conclude that genetic drift has been intense and gene flow low in differentiating populations that follow an island-like pattern of gypsum deposits of the deserts of North America. The interaction between these forces could promote speciation events that in turn would increase regional diversity and may explain the high number of narrow endemics associated with soil restrictions.