Contact zones between marine ecotypes are of interest for understanding how key pelagic predators may react to climate change. We analysed the fine scale genetic structure and morphological variation in harbour porpoises around the UK, at the proposed northern limit of a contact zone between southern and northern ecotypes in the Bay of Biscay. Using a sample of 591 stranded animals spanning a decade and microsatellite profiling at 9 loci, clustering and spatial analyses revealed that animals stranded around UK are composed of mixed genetic ancestries from two genetic pools. Porpoises from SW England displayed a distinct genetic ancestry, had larger body-sizes and inhabit an environment differentiated from other UK coastal areas. Genetic ancestry blends from one group to the other along a SW-NE axis along the UK coastline, and showed a significant association with body size, consistent with morphological differences between the two ecotypes and their mixing around the SW coast. We also found significant isolation-by-distance among juveniles, suggesting that stranded juveniles display reduced intergenerational dispersal, while adults show larger variance. The fine scale structure of this admixture zone raises the question of how it will respond to future climate change and provides a reference point for further study.