We used Random Amplified Polymorphic DNA (RAPD) to investigate genetic variation in eight populations of the vernal pool endemic Navarretia leucocephala Benth. in eastern Washington. Five of the populations were subspecies minima, collected in Spokane County. The other three populations were subspecies diffusa, a recently described taxon known only from adjacent Lincoln County in eastern Washington. We also sampled a nearby vernal pool population of N. intertexta (Benth.) Hook., a closely related species whose range overlaps with N. leucocephala. Distances among the sampled pools ranged from a few tens of meters to 80 km. The populations differed in their levels of genetic variation, with proportions of polymorphic loci ranging from 10% to 55% and mean gene diversities from 0.05 to 0.30. Analysis of Molecular Variance (AMOVA) among the eight N. leucocephala populations showed significant spatial structuring, with 52% of the observed genetic variation due to differences between the Spokane County and Lincoln County populations. Within each county, 10% − 34% of the genetic variation was due to differences among populations. Estimates of Φ_ST indicated significant population differentiation among all populations of N. leucocephala (Φ_ST = 0.65), but the degree of differentiation varied with interpopulation distance. Populations 35–250 m apart were generally not differentiated. At a distance of 1100–1800 m, some populations showed significant differentiation and others did not. Populations 80 km apart were significantly differentiated. On a distance-based phenogram, N. intertexta separated clearly from the N. leucocephala populations, which also grouped by subspecies, suggesting that the morphological features used to differentiate the taxa are paralleled by genetic differences.