Contact zones between ecotypes are windows for understanding how species may react to climate changes. We analysed the fine scale genetic and morphological variation in harbour porpoises (Phocoena phocoena) around the UK by genotyping 591 stranded animals at 9 microsatellite loci. The data were integrated with a prior study to map at high resolution the contact zone between ecotypes in the northern Bay of Biscay. Clustering and spatial analyses revealed that UK porpoises are derived from two genetic pools with porpoises from the southwestern UK being genetically differentiated, and having larger body-sizes compared to other UK areas. Southwestern UK porpoises are admixed between southern and northern ecotypes with a contact zone extending from the northern Bay of Biscay to the Celtic Sea and Channel. Around the UK ancestry blends from one genetic group to the other along a SW-NE axis, correlating with body size variation, consistent with morphological differences between the two ecotypes. We also detected isolation-by-distance only among juveniles but not in adults, suggesting that stranded juveniles display reduced intergenerational dispersal. 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.