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Semiaquatic flies (Diptera, Nematocera) are an ecologically important and species rich group of insects within the boreal and arctic biomes. Community structure, species richness and abundance of semiaquatic flies were studied in three habitat types (aapa mires, springs and headwater streams), totaling 19 study sites, within the subalpine ecoregion of northern boreal Finland. Concordance of semiaquatic fly species composition with plant assemblages (higher plants and mosses), and geographical and environmental distance matrices were also studied. The collected insect material consisted of 94 species and 9038 specimens. According to non-metric multidimensional scaling ordination (visual inspection), multi-response permutation procedure and analysis of similarity tests, fly assemblages of aapa mires were clearly different from those of springs and headwater streams, but no differences were found between spring and headwater stream assemblages. The cumulative number of species was highest in headwater streams. Alpha diversity varied within the habitat types but was generally highest among headwater streams. Semiaquatic fly communities of headwater streams were the most abundant (number of specimens) and their rank-abundance distributions were relatively skewed; assemblages of aapa mires were less abundant and rather even. Community composition of combined plant material (219 taxa), higher plants (116 taxa) and mosses (103 taxa) were all in concordance with the flies; the strongest matrix correlation was found between higher plants and flies (Mantel test). The influence of geographical distance of the study sites to species composition was statistically significant but rather weak; instead, much stronger concordance was noted with environmental variables (Mantel test). Plants, especially higher plants, may be potential surrogates for semiaquatic fly assemblage composition. However, more studies of community concordance in a larger geographic area and within one habitat type are needed.