Morphological differentiation and microhabitat segregation of two ecologically similar populations of pelagic planktivorous fishes, Coregonus albula and the smaller Coregonus fontanae, were studied in Lake Stechlin (northern Germany). Both populations performed diel vertical migrations, although C. fontanae was always situated in deeper pelagic water than C. albula both during day and night. Landmark-based geometric morphometrics revealed that sympatric C. albula and C. fontanae differ in external morphology, with main differences found in head length and eye position, as well as in length and width of the caudal peduncle. Moreover, while C. albula has a similar morphology over all sizes, the shape of C. fontanae changes with size. Accordingly, the morphology of the two is most different at smaller size. Although the morphological differences may reflect adaptations to the slightly differing microhabitats of the two populations, there is no conclusive evidence that this correspondence between ecology and morphology is the main mechanism behind the coexistence of the closely related coregonids in Lake Stechlin.