This study aimed to identify the biogeographical and environmental factors affecting the biodiversity of endemic aquatic species (i.e., Ephemeroptera, Plecoptera and Trichoptera; EPT). We used data collected from 714 sampling sites combined with 39 environmental factors. Ten EPT endemic species were identified. The sampling sites grouped into four clusters based on the similarities of the endemic EPT assemblages using a hierarchical cluster analysis. Non-metric multidimensional scaling (NMS) revealed the differences among the four clusters, with the first three axes being strongly related to annual average, August, and January temperatures, as well as altitude. The random forest model identified geological and meteorological factors as the main factors influencing species distribution, even though the contributions of environmental factors were species-specific. Species with the lower occurrence frequency (i.e., Pteronarcys macra
, Kamimuria coreana
, and Psilotreta locumtenens
) mainly occurred in the least-disturbed habitats. P. macra
represents a priority conservation species, because it has a limited distribution range and is highly vulnerable to anthropogenic disturbance. Our results support the need for an environmental management policy to regulate deforestation and conserve biodiversity, including endemic species.
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