Quantifying genetic structure and levels of genetic variation are fundamentally important to predicting the ability of populations to persist in human-altered landscapes and adapt to future environmental changes. Genetic structure reflects the dispersal of individuals over generations, which can be mediated by species-level traits or environmental factors. Dispersal distances are commonly positively associated with body size and negatively associated with the amount of degraded habitat between sites, motivating investigation of these potential drivers of dispersal concomitantly. We quantified genetic structure and genetic variability within populations of ten bee species in the tribe Euglossini across fragmented landscapes. We genotyped bees at thousands of SNP loci and tested the following predictions: (1) larger species disperse farther; (2) species with greater resource specialization disperse farther; (3) deforested areas restrict dispersal; and (4) sites surrounded by more intact habitat have higher genetic diversity. Body size was a strong predictor of genetic structure, but, surprisingly, larger species showed higher genetic structure than smaller species. The way that deforestation affected dispersal varied with body size, such that larger species dispersed less far in areas with more forest. There was no effect of geographic distance on dispersal, and sites with more intact habitat had higher genetic diversity. These results challenge the dominant paradigm that individuals of larger species disperse farther, motivating further work into ecological drivers of dispersal for bees.