Plant populations are able to undergo very localized adaptive processes, that allow continuous populations to adapt to divergent habitats in spite of recurrent gene flow. Here, we carried out a genome scan for selection through whole-genome sequencing of pools of populations, sampled according to a nested sampling design, to evaluate microgeographic adaptation in the hyperdominant Amazonian tree Eperua falcata Aubl. (Fabaceae). A high-coverage genomic resource of ~250 Mb was assembled de novo and annotated, leading to 32 789 predicted genes. 97 062 bi-allelic SNPs were detected in 25 803 contigs were detected, and a custom Bayesian model we implemented to uncover candidate genomic targets of divergent selection. A set of 290 divergence outlier SNPs was detected at the regional scale (between study sites), while 185 SNPs located in the vicinity of 106 protein-coding genes were detected as replicated outliers between microhabitats within regions. These genes possibly underlie ecologically important phenotypes and tend to indicate that adaptation to microgeographic habitat patchiness would affect genomic regions involved in a variety of physiological processes, among which plant response to stress (for e.g., oxidative stress, hypoxia and metal toxicity) and biotic interactions. Identification of genomic targets of microgeographic adaptation in the Neotropics supports the hypothesis - frequently raised at the community level - that local adaptation would be a key driver of ecological diversification, probably operating across multiple spatial scales, from large- (i.e. regional) to microgeographic- (i.e. landscape) scales.