Inbreeding in trees can result in inbreeding depression (ID), which may affect adaptation and growth of individuals that originate from self-fertilization and mating among relatives. To investigate how inbreeding can affect seed, and seedling growth, we used microsatellite loci to determine the mating system of a Hymenaea courbaril population and assess traits of seeds and seedlings for the expression of ID. Ninety-nine adult trees were mapped and genotyped and seeds collected from eight trees in a forest fragment in Sao Paulo State, Brazil. Seed length and weight were measured and germinated seedlings that had been grown under nursery conditions were genotyped and measured for height and root collar diameter (RCD) at two-month intervals (7–17 months of age). Individual fixation index was estimated for each seedling, from which they were classified as originating from mating among unrelated parents (tu), related parents (tr), or selfing (s). This classification was confirmed using paternity analysis. Phenotypic means and ID of the measured traits were calculated for each determined s, tr, and s+tr group. Mating was not random due to the occurrence of self-fertilization (1.3%), mating among relatives (5%), and correlated mating (15.6%). Biparental inbreeding was attributed to significant spatial genetic structure up to 250 m. The mean fixation index within familieswas significantly higher in seedlings (0.184) than in adults (-0.035), indicating ID from seedling to adult stages. The ID varied among seed and seedling traits throughout the study and between mating groups. Self-fertilization resulted in greater ID for seed length (8.5%) and weight (21.3%) than for tr (<7%). The ID for height and RCD of selfed individuals tended to decrease over the course of the study. The values for ID for seedling height and RCD of the s group were greater (15.8–25.6% for both traits) than for the tr group (3.1–8.2%), with a total (s+tr) similar between height (7.6–9.4%) and RCD (8.1–10.5%). We recommend that seed collection is conducted across a large number of forest fragments in the region where the restoration is to be implemented, preferably in forests that are connected or as close as possible to other remnants, to mitigate the effects of ID in future generations. Seeds must be collected from a minimum of 47H. courbaril trees, respecting a minimum distance of 250 m between each tree to avoid collection of seeds from related individuals.