Plant phylogeny, diversity, and production of germination inhibiting chemicals can be used as patterns for inferring key drivers of plant community construction and assembly. We conducted the study in a restoration area of Atlantic Rainforest from Southeast Brazil. In this context, we aimed to investigate community assembly rules by simultaneously evaluating the relationships of species with a phylogenetic, functional, and ecophysiological (allelopathy) approach and multifaceted β diversity (taxonomic, phylogenetic, and functional). We measured the plant canopy height and diameter at soil height for all individuals and determined successional group and dispersal syndrome for all species regenerating in open areas and below 18 adult individuals of each tree species Bixa atlantica Antar & Sano, Inga laurina (Sw.) Willd., Joannesia princeps Vell. and Senna multijuga subsp. multijuga var. verrucosa (Vogel) H.S.Irwin & Barneby. Phylogenetic and functional indexes of community structure were calculated with the net relatedness index and the nearest taxon index. Taxonomic, phylogenetic, and functional diversities (respectively, TD, PD, and FD) for the regenerating community in each area were calculated and pairwise comparisons were made for TD, FD, and PD components of β diversity. Tests of tree species allelopathy derived from leaf extract were performed with seeds of Lactuca sativa L. (Asteraceae). The effects of diversity and extracts on seed germination were analyzed using generalized linear models. The phylogenetic and functional structure of the regenerating communities under the four tree species did not differ from random for the four studied tree species. The PD was significantly higher for the communities that regenerated under Joannesia, while the FD was higher under both Joannesia and Senna, compared to communities from open sites, evidencing a facilitation mechanism for these two species. Only Senna and Inga differed from random in relation to β TD and β FD, suggesting possible environmental changes in these areas. Seeds irrigated with the extracts of Inga, Joannesia, and Senna inhibited germination in an intermediate way, whereas seeds irrigated with Bixa extract had only 1 % germination, indicating allelopathic effects. In this way, the planted species directly influence the organization of communities that regenerate below their canopies. It is therefore important to choose species that can contribute to improving diversity, and thus favor the success of restoration projects.