Pithecophaga jefferyi Ogilvie-Grant 1896 or the Philippine Eagle is endemic to the Philippines, and is currently listed as an IUCN “critically endangered” species. There is currently an urgent need for genetic information to enhance conservation breeding and preserve the genetic diversity of this species. In this study, we explored the use of mitogenome sequencing as a cost-effective alternative for the genetic studies of Philippine Eagles. Analysis of partial mitogenomes revealed a mean nucleotide diversity of 0.10 to 0.16 from the 27 samples sequenced. This is much lower compared to most threatened bird species. Furthermore, we also observed that most samples belong to a single genetic cluster based on k-means clustering of the pairwise genetic distances, although we detected potentially two distinct subpopulations which was supported by an isolation by distance analysis. Nevertheless, some Philippine Eagle individuals showed distinct nucleotide profiles, with eagles from three key biodiversity area dyads exhibiting high FST, indicating potential genetic differentiation. This suggests limited gene flow between these KBAs, but also their potential use to reinforce the nucleotide diversity in Philippine Eagle captive breeding programs. Finally, phylogenetic analysis of Philippine Eagles and other members of the Order Accipitriformes corroborates previous findings on the non-monophyletic status of the subfamily Circaetinae or the snake-eagles. Altogether, we demonstrate the utility of mitogenomes in assessing the genetic diversity and evolutionary relationships of avian species. Given the huge per-sample cost of whole genome sequencing, the approach utilizing mitogenome sequencing provides a cost-effective alternative to facilitate genetic studies of animals. We therefore anticipate an increasing utility of mitogenomes in population studies for biodiversity and genetic conservation research in the Philippines.