The tympanoperiotic complex of a blue whale Balaenoptera musculus is described and compared to the homologous structures in the other extant and fossil baleen whale species. The periotic and the tympanic bulla represent informative anatomical regions in both functional and phylogenetic studies and for this reason a micro-CT scan of the bones was performed in order to better characterize their external aspect and to reconstruct the inner structures. In particular, the cochlea, the semicircular canals and associated portions of the periotic are reconstructed so that these structures may be used in phylogenetic analyses. We observed that the blue whale periotic is characterized by the presence of a strong dorsal protrusion which is posteriorly bordered by a previously undescribed morphological character that we name the posterotransverse fossa. The peculiar shape of the anterior process and the en echelon organization of the posterior foramina of the pars cochlearis are also described and compared. From a phylogenetic perspective, the blue whale is confirmed to be closely related to the fin whale, Balaenoptera physalus, but it is suggested, based on ear bone characters only, that it diverged before the other balaenopterid species in the phylogeny of Balaenopteridae. This placement supports a series of morphological observations suggesting that the extant blue whale was an early-diverging member of Balaenoptera. Our results help to decipher the evolutionary origin of the blue whale, the largest living animal, by allowing new and more detailed morphological analyses of the balaenopterid fossil record.