Variation in morphological traits is generally thought to be cogradient, with environmental effects on phenotypic expression reinforcing genetic differences between populations. We compared body shape between two populations of Atlantic cod (Gadus morhua). Striking shape differences occurred between juveniles from the two populations when reared in a common laboratory environment. However, no difference in body shape occurred between wild-reared juveniles from the two populations, suggesting that the genetic differences between populations were obscured by opposing effects of the environmental differences experienced in the wild. We suggest that much of the genetic diversity in body shape of fishes may be cryptic, with stabilizing selection for the same optimal phenotype resulting in genetic divergence between populations subject to contrasting environmental influences.