Environmental filtering is one of the most prominent community assembly theories.  Under strong environmental filtering, species dispersing into a community are excluded or included according to their environmental compatibility; determined largely by species’ relevant functional traits.  Previous analyses of environmental filtering have taken a whole community approach, identifying communities that are more closely related than expected, indicating high similarity of traits along unknown but key environmental axes.  Other assembly processes, particularly competitive exclusion, can also be involved in a community’s assembly.  When both processes are involved, it may appear that neither process is active if only whole communities are examined.  In communities influenced by both processes, different traits may be involved in maintaining coexisting species.  In this study, we provide evidence for environmental filtering acting differentially at the clade level within Costa Rican plant communities with and without strong community-wide environmental filtering signatures.  We also identify specific dispersal and pollination traits of likely importance for the environmental filtering of specific clades found in particular habitat types.  Traits of potential importance to species persistence in particular habitat types are identified using a novel trait, habitat, clade three-way interaction analysis; a more effective method than the typical method, which relies on multiple two-way analyses.  Our “thc” method reveals traits significantly correlated to clade/habitat combinations, which were not identifiable using the two-way interaction approach.  Our study provides insights into the role of environmental filtering in real plant communities, and whether pollination and dispersal traits contribute to this process in our study system.