GARUDA: the first complete mitochondrial genome of the endangered Javan hawk-eagle (Nisaetus bartelsi) and its phylogenetic relationships within Accipitridae

The Javan hawk-eagle ( Nisaetus bartelsi ), Indonesia’s endemic national bird, endangered keystone predator, lacks genomic data despite severe threats from habitat loss and illegal trade. Here, the first complete mitochondrial genome of N. bartelsi is reported, assembled from Illumina sequencing into a 17,974 bp circular mitogenome. The mitogenome comprises the typical avian set of 37 genes—13 protein-coding genes (PCGs), 22 tRNAs, and two rRNAs, and shows a slightly AT-biased nucleotide composition (T 23.4%, C 32.6%, A 30.0%, G 13.9%; GC 46.5%). PCGs total 10,711 bp and exhibit elevated GC content (48.3%) and pronounced compositional skews (GC skew − 0.40, AT skew 0.06); relative synonymous codon usage reveals a strong preference for A/U-ending codons. The genome includes 22 tRNAs with canonical cloverleaf structures, 2 rRNAs, and two control regions with CR2 harbouring 17 tandem repeats. Phylogenetic analysis places N. bartelsi within Aquilinae (diverged ~ 12.45 Mya, HPD 10.85–13.98 Mya) as sister to S. alboniger (~ 3.36 Mya, HPD 2.83–3.92 Mya), with recent diversification within Miocene-origin Aquilinae. These mitogenomic and phylogenetic results provide a foundation for population genetics, forensic identification, and conservation strategies for this endangered raptor.