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Vocal and phylogenetic research has revealed much hidden species-level diversity in tyrant-flycatchers (Tyrannidae), and field ornithological accounts indicate there is a great deal of additional diversity to be uncovered. Using mitochondrial and nuclear DNA sequences, we screened genetic diversity from across the range of two pan-Neotropical species of elaeniine flycatcher – Camptostoma obsoletum (Southern Beardless Tyrannulet) and Phaeomyias murina (Mouse-coloured Tyrannulet) – for which vocal discontinuities have previously been reported. Our results indicate deep genetic divergences across the Andes in both species, and support a previously proposed separation of trans-Andean populations of P. murina into P. tumbezana. Within C. obsoletum, we additionally uncover a deep genetic break between a trans-Andean clade from dry Tumbesia and one from humid Chocó–Panama, and we fail to detect mitochondrial DNA differentiation in western Amazonian C. o. olivaceum, which has been treated as a distinct form based on differences in voice and plumage from surrounding subspecies. Further molecular and vocal sampling is necessary to confirm the division of C. obsoletum into three species. [ABSTRACT FROM AUTHOR]