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Macroinvertebrates in forest streams affect the overall health of other streams in the same water system. In this study, we compared differences in the benthic macroinvertebrate community at two headwater streams located at different latitudes in the southern and northern parts of South Korea. We calculated the community temperature index (CTI), which represents the thermal preferences of the benthic communities. Hierarchical cluster analyses (HCA) were conducted to compare the similarities among sampling sites. In addition, we analyzed the relationship between community composition and environmental and community characteristics using non-metric multidimensional scaling (NMDS). Our results showed that CTI was significantly different between the two regions, indicating that these benthic macroinvertebrate communities have different thermal preferences. These two regions were clearly distinguished from each other in the HCA; furthermore, seasonal differences in benthic community composition were observed within each region. The functional feeding groups present in the benthic macroinvertebrate communities were different even though their habitat was similar.