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Verticordia staminosa C.Gardner & A.C.George subsp. staminosa is an extremely rare shrub occurring as an isolated population of similar to 1200 plants on a granite outcrop in the semi-arid agricultural region of Western Australia, separated from its closest relative V. staminosa subsp. cylindracea by 400 km. We aimed to determine a hierarchy of causes for explaining the extremely restricted distribution of subsp. staminosa, and to determine the genetic relationships among populations within both subspecies. We measured allozyme variation in all known populations of the two subspecies. There were exceptionally high levels of genetic divergence between subsp. staminosa and subsp. cylindracea, including an apparent duplication of the gene encoding phosphoglucomutase, leading to an additional gene in subsp. cylindracea. These findings combined with UPGMA analysis indicate a very long period of historical separation, perhaps originating in the early Pleistocene. Genetic variation was partitioned mostly between rather than within populations, with very low levels of genetic variation within populations of both subspecies. For subsp. staminosa we quantified seed production for three consecutive years and demography for five consecutive years. We used transition matrix models to describe the shrub’s population dynamics and stochastic simulations to explicitly compare the effects of low rainfall and disturbance on population viability. Verticordia staminosa subsp. staminosa produces large numbers of seeds each year and has flower to fruit ratios greater than reported for related rare and common congeners. Seedling recruitment occurs in most years, with pulses in the wettest years. The mean finite population growth rate was 1.031. Elasticity analyses showed that population growth rate was more sensitive to stasis of established plants than to seedling recruitment. Population viability declined with lower rainfall and increased fire-related mortality of adult plants. Rarity in subsp. staminosa is best explained by evolutionary history and the interaction of climate change and disturbances such as fire that kill plants. Climatic fluctuations since the late Pliocene might have led to stochastic extinction episodes of populations on other granite outcrops, resulting in the currently restricted distribution. We discuss the implications of our findings for management of the species.