The large interspecific variation in marine mammal skull and dental morphology reflects ecological specialisations to foraging and communication. At the intraspecific level, the drivers of skull shape variation are less well understood, having implications for identifying putative local foraging adaptations and delineating populations and subspecies for taxonomy, systematics, management and conservation. Here, we assess the range-wide intraspecific variation in 71 grey seal skulls by 3D surface scanning, collection of cranial landmarks and geometric morphometric analysis. We find that skull shape differs slightly between populations in the Northwest Atlantic, Northeast Atlantic and Baltic Sea. However, there was a large shape overlap between populations and variation was substantially larger among animals within populations than between. We hypothesize that this pattern of intraspecific variation in grey seal skull shape results from balancing selection or phenotypic plasticity allowing for a remarkably generalist foraging behaviour. Moreover, the large overlap in skull shape between populations implies that the separate subspecies status of Atlantic and Baltic Sea grey seals is questionable from a morphological point of view.