Philornis Meinert, 1890 (Diptera: Muscidae) is a genus of Neotropical dipterans that parasitise birds. The currently used external morphological characters to distinguish between species within this genus present some limitations. We used the second internal transcribed spacer region (ITS2) of the rRNA gene as a molecular marker to differentiate adult specimens of Philornis identified morphologically as Philornis torquans and Philornis seguyi from different localities. Specimens identified as P. seguyi from Magdalena (Buenos Aires Province) showed an ITS2 sequence different from that for P. torquans, whereas all other specimens of P. seguyi had sequences identical to those for P. torquans. These findings do not necessarily confirm that specimens from Magdalena indeed belong to P. seguyi, nor that P. seguyi is a valid species. Instead, they alert us about the potential for species misidentification when using morphological characters alone. The use of molecular approaches to aid the identification of Philornis spp. will shed light on the systematics of this group. P. torquans is reported for the first time in Mendoza Province and Uruguay.