A well-known but largely untested prediction in plant reproductive ecology is that dioecious taxa should produce larger more higher-quality or better-defended seeds than cosexual taxa. Using a data set composed of 972 species in 104 families representing the flora of the Tambopata Wildlife Reserve (Madre de Dios Peru) we evaluated the first component of this prediction examining ecological and evolutionary relationships between breeding system and mean seed size with two kinds of tests. First we conducted cross-species analyses to determine whether species with different breeding systems differed significantly with respect to mean individual seed size. Second we used a hypothesized phylogeny to identify pairs of the most closely related taxa or clades within the Tambopata community that differed with respect to breeding system. Comparing pair members allowed us to determine whether evolutionary divergence in breeding system (between taxa with unisexual vs. cosexual individuals) was consistently associated with evolutionary change in seed size. In both analyses we controlled for potentially confounding effects of growth form by examining these relationships within woody and nonwoody taxa. Cross-species analyses revealed that dioecious species produced larger seeds than cosexual species among woody species shrubs lianas (each growth form analyzed separately) and all species pooled but not among trees. Phylogenetically independent contrasts upheld the significant association between breeding system and seed size among woody taxa lianas and all taxa pooled but not among shrubs. We discuss the implications of our findings for evolutionary hypotheses regarding associations between dioecy and seed size.