Biodiversity encompasses species diversity, which includes species richness and species evenness. High species diversity is known to contribute to community stability and the potential for maintaining healthy ecosystem functioning. However, the most commonly used species diversity indices have some limitations, as they require species-specific abundance data for each community. In contrast, phylogenetic diversity measures the evolutionary distances between species within a community, reflecting ecological and/or evolutionary divergences and niche differences, without requiring abundance data. This study assessed biodiversity by calculating phylogenetic diversity indices for freshwater fishes (19 species) and aquatic insects (49 species) at three sites within Seoraksan and Odaesan National Parks. The aquatic insects studied belong to the EPT group (Ephemeroptera, Plecoptera, and Trichoptera), which are widely used as bioindicators of aquatic ecosystems. Two mitochondrial DNA genes were used as molecular markers: COI and cyt b for fish, and COI and 16S rRNA for the EPT - group. Overall, Odaesan National Park exhibited higher phylogenetic diversity in both fishes and aquatic insects compared to Seoraksan National Park, although this difference was not statistically significant. The highest phylogenetic and species diversity were observed for fish at the OD2 site (Woljeong District) and for the EPT group at the OD1 (Gyebangsan) and SA2 (Jangsudae) sites. Correlation analysis revealed that phylogenetic diversity indices were more positively associated with species richness than species diversity indices. This study serves as a pilot project for establishing standardized methods for assessing biodiversity in national park habitats using phylogenetic diversity. It also aims to inform various policies, such as the development of biodiversity assessment systems and the prioritization of protected areas within national parks.