Incomplete lineage sorting (ILS) generates widespread genomic discordance in rapidly radiating lineages, yet its phenotypic impacts remain poorly understood. Among hominids, over 30% of the human genome supports conflicting phylogenetic trees due to ILS, affecting numerous genes with morphological functions. We present a trait-based approach integrating comparative morphology, population genomics, and functional experiments to identify and validate ILS-affected traits in hominids, often interpreted as convergent adaptations. Phylogenetically incongruent traits are frequent in the craniofacial and appendicular skeletons, highlighting priority areas for ILS investigation and ascertainment bias. This approach requires collaborative models bridging morphological and genomic data gaps in non-human hominid research, illuminating the forces shaping great ape evolution and establishing a roadmap for exploring ILS consequences in diverse taxonomic groups.