Habitat degradation and fragmentation are widespread phenomena in tropical regions. Negative effects on the biota are numerous, ranging from interruption of gene flow among populations, to the loss of genetic diversity within populations, to a decline in species richness over time. Orchid bees (Hymenoptera: Apidae: Euglossini) are of major conservation interest due to their function as pollinators of numerous orchid species and other tropical plants. Here, we used microsatellite markers to investigate the effects of geographic distance and habitat fragmentation on gene flow among populations. Populations of Euglossa dilemma in three geographic regionsthe Yucatán peninsula (Mexico), Veracruz (Mexico), and Florida (USA)-were genetically structured predominantly across the regions, with the strength of differentiation among populations being positively correlated with geographic distance. Within geographic regions only little substructure was found, suggesting that dispersal is substantial in the absence of geographic or ecological barriers. In a second study, patterns of genetic differentiation among eight species of Euglossa were not related to habitat fragmentation following deforestation in southern Mexico (Veracruz). Specifically, most bee populations in the 9,800 ha forest remnant of Los Tuxtlas (Volcano San Martin) were neither differentiated from, nor had less genetic diversity than, populations in near-continuous forest separated from Los Tuxtlas by 130 km of agricultural land. Either occasional long distance dispersal across open areas has buffered the expected genetic effects of fragmentation, or the history of fragmentation in southern Mexico is too recent to have caused measurable shifts in allelic composition.