Abstract The aim of this study was to evaluate the relative contributions of the environment, landscape patterns, and spatial structure to explaining the variation in richness of rare woody species at three levels of rarity (low, medium, and high) and at different grain sizes and spatial extents. We used herbarium records of 195 rare woody species to quantify species richness—overall and for three levels of rarity—of the Yucatan Peninsula, Mexico. We assessed relationships between rare species richness and different sets of explanatory variables (environmental, landscape patterns, and spatial structure of sampling units) using linear regression and variation partitioning analyses at three grain sizes (625, 400, and 225 km2 ). We also conducted a principle coordinates of neighbor matrices analysis to allow interpretation of the results in terms of different spatial extents. The percentage of variation in rare species richness explained by the models was highest for the largest grain size and spatial extent. At the larger extents, rare species richness was explained mainly by the environment, whereas landscape patterns played a more prominent role at the local extent. Landscape patterns also contributed more to explaining species richness at low to medium levels of rarity, whereas the richness of extremely rare species was better explained by spatial structure. We conclude that the relative contribution of the factors explaining the variation of rare species richness depends on both grain and extent, as well as on the level of rarity. These results underscore the importance of considering the different components of scale (grain and extent) as well as different levels of species rarity in order to better understand the patterns of distribution of rare species richness and to be able to frame appropriate conservation strategies.