<p>Palms play crucial ecological and economic roles, and <i>Syagrus romanzoffiana</i> is a widely distributed species in South America. Despite its ecological importance and economic potential, population-level genetic studies of this palm remain limited. Here, we assessed genetic diversity, population structure, and signatures of local adaptation across distinct vegetation types in Brazil and Paraguay using 24,859 single nucleotide polymorphisms (SNPs) derived from genotyping-by-sequencing (GBS). We analyzed 91 individuals from 8 populations, revealing high genetic diversity within populations and moderate differentiation among them. Observed heterozygosity was generally high, with some populations showing an excess of heterozygotes, consistent with outcrossing and gene flow. Pairwise F_ST and AMOVA confirmed that most variation is maintained within populations, while genetic structure analyses highlighted the influence of vegetation type on differentiation, with <i>restinga</i> populations displaying distinct genetic signatures. Despite geographic proximity, some populations exhibited greater divergence associated with local environmental conditions, supporting isolation by environment. Environmental association analyses (LFMM and RDA) identified SNPs associated with temperature and precipitation, indicating adaptive genomic differentiation across contrasting habitats. Together, these findings demonstrate how habitat type and climate jointly shape neutral and adaptive genetic variation in <i>Syagrus romanzoffiana</i>, providing a genomic baseline relevant for conservation, restoration, and seed sourcing strategies under ongoing habitat fragmentation and climate change.</p>