The high rates of substitution in mitochondrial genes and assumed neutrality of their polymorphisms encourage the use of mtDNA in phylogenetic and evolutionary studies. However, the true nature of the mitochondrial genome and its influence upon processes of adaptation and speciation are not fully understood, particularly where associations appear to exist between ‘neutral’ mitochondrial haplotypes and characteristics that are under direct selection. In snails, one such characteristic is shell shape. In this study a mitochondrial haplogroup is found to be confined towards one end of the spectrum of shell variation in an ecotype of the rough periwinkle Littorina saxatilis on a shore in the British Isles. We speculate that this may signal hitherto unexpected selection, and perhaps even some reproductive isolation between this group and the rest of the population, and we propose intergenomic coadaptation as a possible mechanism through which this occurs.