A craniometric study was conducted on a sample of 209 specimens of the Iberian desman, representing the main areas of the species’ distribution range: Pyrenees, Iberian System, Cantabrian area, Atlantic area, and Central System. No age differences were found in the sample but, conversely to previous reports, results revealed a slight sexual dimorphism in size. Multivariate size and shape analyses performed on both sexes separately indicated that the Pyrenean sample is the one that differs most from the others. Skull of specimens from the Atlantic area was smaller than those from the Cantabrian area, Iberian System, and Central System, and very similar in size to the desmans from the Pyrenees. Nevertheless, in the canonical plots for size and shape both males and females from the Atlantic area clearly fall within the range of variation of non-Pyrenean desmans. Although our analyses showed that there is a general morphological skull differentiation between the two classic subspecies of the Iberian desman described in the literature, it is clear that further morphological and genetic studies are needed to clarify the infraspecific taxonomy of this species fully.