Offspring from matings between near neighbors may exhibit lower fitness relative to offspring from more distant matings due to spatial structuring of populations resulting from limited dispersal of pollen and seed. This response, which can be interpreted as inbreeding depression, is studied in the rare species, Eupatorium resinosum, and a closely related congener, E. perfoliatum, through the use of hand pollinations representing three distance classes (near-within a population, far-within a population, and between populations) and an assay of the offspring in an experimental plot. Early traits such as seed mass and first-year stem length were not significantly affected by the cross type, although they were affected by maternal parentage. Size and reproduction in the second field season increased with increased pollen donor distance from the maternal plant. Cross type was significant for many traits in the second field season, indicating inbreeding depression in crosses of neighbors (for E. resinosum) and hybrid vigor between populations (both species). This suggests that the rare species, E. resinosum, had a more spatially structured population than E. perfoliatum. The implications of these results for conservation of rare species indicate that protection of habitats sufficient for large populations is necessary to maintain genetic diversity since each population likely consists of many smaller subpopulations.