The mapping of developmental variation into variation among adults has implications for evolutionary and developmental biology. Here we study the developmental basis of morphological variation in adult fishes with geometric morphometric analyses. In Iceland Arctic charr (Salvelinus alpinus) can be found in many landlocked lakes and springs. The most drastic example are the four sympatric morphs of Lake Thingvallavatn: two benthic a small (SB) and large one (LB) as well as two limnetic a planctivourious (PL) and a piscivorous (PI). In this study we estimated the variation in placement and migration of the developing eyes and ethmoid plate in three of the Thingvallavatn morphs (LB, SB and PL). Furthermore we examined the effects of morph and sex on shape of adult SB and PL charr. We used thin plate spline approaches to capture the shape for both embryos and adults. The effect of variables such as morph and time and in the adults sex and weight as a covariate were evaluated with ANOVA. The morphometric analyses highlight both migration of the eye and the growth of the ethmoid plate during development. The data suggests substantial differences between the morphs during early development, though there certainly is high degree of variation among indviduals and samples. There is also significant shape differences between adults, depending on morph and sex. One axis of shape variation is also strongly correlated with size (and weight). Furthermore, the weight distribution of small benthic females is broader than for the small pelagics.