Phylogenetic relationships are often challenging to resolve in recent/younger lineages when only a few loci are used. Ultra-conserved elements (UCEs) are highly conserved regions across taxa that help resolve shallow and deep divergences. We utilized UCEs harvested from whole genomes to assess the phylogenetic position and taxonomic affiliation of an endangered endemic owlet in the family Strigidae, the Forest Owlet Athene blewitti. The taxonomic placement of this species has been revised multiple times. A multigene study attempted to address the question but showed a discrepancy across datasets in its placement of species within the genus Athene. We assembled a dataset of 5018 nuclear UCE loci with increased taxon sampling. Forest Owlet was found to be an early split from the Athene clade but sister to other Athene, consistently across three approaches maximum likelihood, Bayesian and the multispecies coalescence. Divergence dating using fossil calibrations suggests that the Athene lineage split from its ancestor about 7.6 mya, and Forest Owlet diverged about 5.2 mya. This estimate is consistent with previous multigene approaches and confirms the role of climate-aridification across the Indian peninsula in species diversification. Despite osteological differences from other Athene, we suggest placement of the Forest Owlet as a member of the Athene to emphasize its evolutionary relationship.