The lowland Amazon rainforest houses some of the greatest tree diversity on earth. While the vast majority of these species are rare, a small number are common and widespread. Several recent studies have found that some dominant species are actually composed of multiple independently evolving lineages. However, the extent to which widespread and common Amazonian tree species actually include multiple clades, each on their own unique evolutionary trajectory, is unknown. Here we investigate the extent to which lineage divergence may be occurring within Protium subserratum (Burseraceae), a common and widespread tree species that is monophyletic with populations exhibiting genotypic and phenotypic differences associated with environment and geography. Utilizing a combination of phylogenomic and population genomic methods with sampling from across the range using herbarium specimens, we found that P. subserratum contains at least eight distinct clades defined by geography and environment. Specialization onto white-sand soils has evolved independently at least two times within the species; however, phenotype is not correlated with soil type. Finally, cryptic diversity at the base of the Andes is associated with elevational shifts. Together these results lend support to the hypothesis that common and widespread Amazonian species may contain multiple, independently evolving lineages.