Sexual dimorphism is a very common strategy in polygamous mammals. In mustelids, sexual size dimorphism (SSD) is present in several species, while sexual shape dimorphism (SShD) is not as common. The Eurasian otter is a semiaquatic mustelid, exclusively feeding on aquatic prey, mainly fish, amphibians, and crustaceans. It is well-known that male otters tend to be larger, whereas information on SShD is contrasting. We used a 3D geometric morphometric approach to investigate SSD and SShD in three genetically distinct populations of otters located in Northern, Central and Southern Sweden. We analyzed 71 otter skulls (M = 41, F = 30), using photogrammetric techniques to produce 3D models of each skull, placing 30 3D landmarks on each model. We found that sexual dimorphism varies among populations. Neither SSD nor SShD occurred in the North, only SSD occurred in the Centre, and both SSD and SShD are present in the South of Sweden. Allometric trajectories of males and females from the North population differed from those of the other two populations. Our results highlighted a great variability in sexual dimorphism in Swedish Eurasian otters, that probably derives from different responses to prey availability and historical contingencies.