In southern Canada, peatlands are usually present as disjunct fragments, representing islands of northern biodiversity in a temperate zone. These southern peatland fragments are particularly threatened by human disturbance. Although arthropods are abundant and ecologically diverse in peatlands and occupy all trophic levels, fundamental research on the diversity of terrestrial arthropods in bogs is sporadic and little is known about their response to habitat fragmentation and disturbance. Six bogs in southern Quebec and northern Vermont, ranging in size from 12 to 900 hectares were sampled in the summer of 2006 to test the prediction that Diptera diversity decreases as bog area decreases. Analyses are based on 5500 specimens in target families of higher Diptera, representing 270 species in 28 families. A significant, positive correlation between habitat size and species richness was not found and the most species-rich and diverse sites were of intermediate size. Diptera communities were slightly separated at the site level though differences in species composition were not based on bog size. Indicator species analysis shows no species associations with the two smallest sites, twelve species were associated with intermediate-sized sites and ten species were associated with the largest site. Our results suggest that bogs of intermediate size are able to support diverse Diptera communities though analysis of surrounding land use and vegetation variables is needed to further understand the Diptera communities that inhabit bogs.