Phylogenetic diversity (PD) is defined as the sum of the total lengths of branches of species in phylogenetic tree. Unlike typical metrics based on number of species and individuals, phylogenetic diversity could evaluate ecological and life-history trsits of species in community. This study compared and analyzed the ecological similarity and differentiation in terms of biodiversity through phylogenetic diversity of birds in both Geumgangsan and Seoraksan National Parks, which are connected to ecological network for board area on natinoal land. Phylogenetic diversity of birds investigated from both Geumgangsan and Seoraksan National Parks was found to be similar overall, confirming the ecological connectivity between biodiversity aspects. In particular, Jaccard’s similaritiy analysis showed that forest-dwelling birds were highly similar between national parks whereas waterbirds differed. Because Geumgangsan National Park is adjacent to the East sea, there were more waterbirds. Although we found ecological signifcant in bird diversity between national parks, this study has limitation that our analyses considered no environmental characteristics as habitat factors. However, to minimize the limiations of bird surveys conducted in North Korea, phylogenetic diversity was identified as possible method of the assessment and we discussed on this.