The Javan hawk-eagle, Nisaetus bartelsi (Stresemann, 1924), is an endemic raptor of Java, Indonesia, whose population is listed as endangered. As part of conservation efforts, phylogenetic reconstruction is necessary to understand its evolutionary history and relationships. This study aims to investigate the phylogenetic relationship between N. bartelsi and other members of the genus Nisaetus, as well as to evaluate the resolution of phylogenetic trees within the subfamily Aquilinae using five mitochondrial DNA markers: COI, cyt-b, ND2, ND4, and ND5. Genetic data were obtained from a blood sample of N. bartelsi and compared with sequences of other members of Aquilinae obtained from GenBank. Phylogenetic tree reconstruction using Maximum Likelihood (ML) and Bayesian Inference (BI) recovered N. bartelsi as the sister-taxon of N. alboniger and N. nipalensis with robust support, in contrast to previous studies which placed N. bartelsi as the sister-species of N. alboniger. Furthermore, the sampled representatives of the genera Nisaetus, Aquila, and Hieraaetus were recovered as monophyletic groups. The topology distinctly separates the Aquila-Hieraaetus clade from the Nisaetus-Spizaetus clade. Among the five markers, ND2 exhibited the highest proportion of variable sites (37.7%) and parsimony-informative sites (22.7%). Additionally, species delimitation analysis using Automatic Barcode Gap Discovery (ABGD) recovered N. bartelsi as a distinct molecular unit, a result congruent with its current taxonomic status despite its morphological similarities to other Sundaic hawk-eagles.
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2026 The Author(s). Integrative Conservation published by John Wiley & Sons Australia, Ltd on behalf of Xishuangbanna Tropical Botanical Garden (XTBG).
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