Dispersal is a major determinant of connectivity between communities that may modulate the importance of environmental and spatial processes on taxonomic composition. While wind is likely to influence transport distance, rate and direction for numerous species, its effects on community composition remain poorly understood.Using eigenvector-based spatial analyses, we investigated the influence of wind flows, estimated by mesoscale models, on the spatial structure of benthic macroinvertebrate assemblages with contrasting flying abilities in high Andean wetlands (26–32°S). We further quantified the relative importance of local and regional processes through a variation partitioning approach.The influence of environmental heterogeneity was prevalent and of relatively similar amplitude in both flying and non-flying assemblages. Significant spatial structure more strongly driven by wind flows than by Euclidean schemes was detected for both assemblages. As expected, the highest levels of spatial structure were observed for the flying macroinvertebrate assemblage and they occurred at a much larger spatial scale in this group, suggesting a greater dispersal aptitude of the flying taxa.Our results show that environmental effects are predominant in shaping the spatial structure of macroinvertebrate communities in high Andean wetlands, as generally found in other systems. They also demonstrate the significance of wind flows in regulating high-altitude wetland macroinvertebrate communities and illustrate the importance of considering adequate spatial models and biological characteristics of species to advance our understanding of community patterns.