Environmental heterogeneity across the landscape can cause lineage divergence and speciation. The Geonoma macrostachys (Arecaceae) species complex has been proposed as a candidate case of ecological speciation in Amazonia due to evidence of habitat partitioning and pre-zygotic reproductive barriers between co-occurring morphotypes at a local scale. In this study, we provide a continent-wide perspective of the divergence patterns in G. macrostachys by integrating data from morphological traits, target sequence capture, climate, soil and reproductive biology. A morphometric analysis revealed four morphogroups, defined by traits related to leaf shape. A coalescence-based phylogenetic analysis did not recover the morphogroups as monophyletic, indicating independent evolution of leaf shape across geographical space. We demonstrate scale-dependent habitat differentiation for two of the morphogroups, in which segregation driven mostly by climate was complete at the regional scale but incomplete at the continental scale. Contrary to previous evidence of reproductive isolation in the form of different pollinators and flowering times between sympatric G. macrostachys forms in Peru and Ecuador, these were not found in Colombia, suggesting reproductive barriers have evolved multiple times across its geographical range. Taken together, our findings suggest that ecological divergence and local adaptation is driving diversification in G. macrostachys, and that hyperdiverse regions such as Amazonia are probable arenas for ecological divergence in sympatry.