Palms (family Arecaceae) are integral to understanding the evolution of tropical rainforests due to their long evolutionary history, high species richness, and hyper dominance in these ecosystems. Some palm genera, like Geonoma, are regionally and locally species-rich and abundant in Neotropical rainforests, but factors contributing to their divergence and ultimately their diversification remain poorly explored. A recent phylogenomic study identified the Geonoma undata complex, with high levels of genetic distinctiveness of different geographically proximal groups, describing it as a hyper-cryptic radiation. Here, we seek to disentangle the factors that contribute to genetic divergence in the G. undata cryptic species complex in the Northern Colombian Andes, where various forms ascribable to different taxonomic, morphological, and genetic groups exist. To address this, we pursued three main aims using nuclear single nucleotide polymorphisms distributed along over 4,000 genomic regions from 156 individuals. (i) We identified populations and used diversity metrics to understand evolutionary scenarios across pairwise comparisons of those populations. Geographically sympatric populations display evidence for allopatric selection that is likely explained by elevational segregation. (ii) Tajima's D was used to infer broad genomic trends in selection and drift. In general, divergence between populations is enhanced by drift through population expansions. (iii) Lastly, we used outlier divergence and selection statistics to identify genes with outstanding divergence under significant positive selection. Two genes were identified that fit this description and are found to play functional roles in phenology, such as light response and flowering time.