Geographic barriers, such as mountain ranges, impede genetic exchange among populations, promoting diversification and speciation. The effectiveness of these barriers in limiting gene flow varies between lineages due to each species’ unique dispersal modes and capacities. Our understanding of how the Andes orogeny contributes to species diversification comes from well-studied vertebrates and a few insects, neglecting organisms unable to fly or walk long distances. Additionally, although the Andean altitude is usually assumed to be the driver of diversification, it is not often formally tested. This limits our understanding of how landscape changes, particularly altitude, influence population structure. Some arachnids, such as the colorful spider Gasteracantha cancriformis have been hypothesized to disperse long distances via ballooning (i.e., using their silk to interact with the wind). Still, we do not know how the environment and geography shape its genetic diversity. To address this question, we sampled thousands of loci across the distribution of this spider and implemented population genetics, phylogenetic, and landscape genetic analyses. We identified two genetically distinct groups structured by the Central Andes and a third less structured group in the northern Andes that shares ancestry with the previous two. This structure is largely explained by the elevation along the Andes, which decreases in some regions, facilitating cross-Andean dispersal and gene flow. Our findings support that elevation in the Andes plays a major role in structuring populations in South America, but the strength of this barrier can be defeated by organisms with long-distance dispersal modes together with altitudinal depressions