The avian genus Ficedula has been a model system for studying speciation, genomics, biogeography, and the evolution of migratory behavior. However, no multi-locus molecular phylogenetic hypothesis exists for the genus. We expanded taxon and character sampling over previous studies and produced a robust hypothesis of relationships for the genus. Many previous findings, such as the inclusion of Muscicapella and exclusion of Ficedula monileger from the genus, were verified, but many relationships differed compared to previous work. Some of the differences were due to increased sampling, but others were due to problematic sequence data produced from DNA extracted from historical museum specimens. The new phylogenetic hypothesis resulted in a simpler biogeographic scenario with fewer transitions between regions and fewer transitions between seasonally migratory and resident character states. Notably, all species endemic to the Philippines and Wallacea formed a clade, which included Ficedula dumetoria of the Sunda Shelf and Lesser Sundas. In addition, Ficedula hyperythra was not monophyletic; samples from Philippine populations formed a clade distantly related to a clade that comprised all other sampled populations.