Plesiorycteropus (Malagasy aardvarks) is the sole genus belonging to an extinct mammalian order, the Bibymalagasia, that lived in Madagascar in the Quaternary. Its systematic and phylogenetic position is controversial because Plesiorycteropus morphologically resembles aardvarks (Tubulidentata), whereas a recent molecular analysis proposed that it belongs to Tenrecoidea, along with Tenrecidae (tenrecs and otter shrews) and Chrysochloridae (golden moles). This context of competing phylogenetic hypotheses is stimulating for the investigation of new characters for phylogenetic inferences. Here we used the noninvasive methods of micro-computed tomography scanning, digital reconstruction, and three-dimensional geometric-morphometric analysis of shape to investigate the morphology of the bony labyrinth (osseous inner ear) of the holotype skulls of both known species of Bibymalagasia: Plesiorycteropus madagascariensis and P. germainepetterae. Firstly, by comparisons with their extant relatives, we find that the characters of the bony labyrinth that distinguish P. madagascariensis and P. germainepetterae could only represent intraspecific variation. Secondly, we find that the bony labyrinth of Bibymalagasia is distinctive from those of other Afrotherians examined, supporting their ordinal distinctiveness. Indeed, the principal component analysis on labyrinthine shape data shows that the bony labyrinths of both Plesiorycteropus species are in fact intermediate between those of tubulidentates and other Afrotherian insectivores. Finally, we investigated the evolution of the secondary common crus (partial fusion of the lateral and posterior semicircular canals) in Afrotherians and found that this character is present in tubulidentates and potamogaline tenrecs, supporting the hypothesis that its presence is primitive for Afrotherians. In contrast, Plesiorycteropus displays the derived condition (i.e., loss of the secondary common crus).