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We investigated the relationship between the seed bank and aboveground vegetation and the effect of microhabitat (shrub interspace or beneath shrub) and aboveground community phase (high or low perennial bunchgrass cover) on the seed bank of a Great Basin Desert sagebrush community. The seed bank and aboveground vegetation differed in their most dominant species, resulting in moderately dissimilar species compositions as determined by Sørensen’s similarity index and Bray–Curtis distance. In contrast, comparing the seed bank species composition to the aboveground vegetation structure (functional groups) using non-metric multidimensional scaling (NMDS) revealed a correspondence between the two communities. Shrub seed densities were higher beneath shrubs. Neither microhabitat nor community phase explained variation in total seed density or species richness. Therefore, our measures of the aboveground vegetation did not influence seed density across functional groups or species richness, and the similarity between the seed bank and aboveground vegetation varied depending on the aboveground organizational level used in comparisons.