Headwater streams provide various microhabitats, resulting in high diversity of macroinvertebrate community. In this study, we compared the differences of communities between two adjacent headwater streams (Jangjeon stream (GRJ; GRJ1-GRJ5) and Haanmi stream (GRH; GRH1-GRH3)) in Jungwang and Gariwang mountains, Gangwon-do and evaluated the effects of habitat condition to the macroinvertebrates community composition. In order to characterize the macroinvertebrate communities and extract influential environmental factors, we applied to Cluster analysis (CA), Indicator species analysis and Non-metric multidimensional scaling (NMDS). Total 33,613 individuals in 3 phyla, 5 classes, 13 orders, 51 families, and 114 taxa (genera or species) were collected. Gammarus sp. was dominant at the upper stream of GRJ, whereas Chironomidae spp. was abundant at GRH and the downstream of GRJ. The CA classified samples into six clusters (1-6) reflecting spatial and temporal variation of benthic macroinvertebrate communities. Benthic macroinvertebrate community composition was significantly different between two adjacent streams. Sweltsa sp. 1, Psilotreta kisoensis, Rhyacophila shikotsuensis and Serratella setigera were identified as representative indicator species for clusters 1, 2, 3 and 5, respectively. Similar to CA results, NMDS revealed the spatial and temporal differences of benthic macroinvertebrate communities, indicating the difference of community composition as well as microhabitat condition. Forest composition, proportion of boulders (>256 mm), and water velocity were main factors affecting the macroinvertebrate community composition.