Two previously described lacustrine cisco Coregonus spp. morphs [i.e. a small (<300 mm fork length, LF), low-gillraker (≤44) morph and a large (≥300 mm LF), high-gillraker (≥45) morph] from Great Slave Lake, NT, Canada, were found to be synonymous with cisco Coregonus artedi. Geometric body shape did not differ between the two size classes nor could they be differentiated by 24 size-corrected linear measurements, indicating that the two groups had similar phenotypes. Strong, positive correlations between all linear characters and geometric centroid size (a composite variable of fish body length, mass and age) suggested that body morphology changed with age as fish grew. Total gillraker number (NGR) increased with LF according to: NGR = 36·3 + 0·034LF. Differences in gillraker number and phenotype with age and size were explained by shifts in habitat and trophic resource use. Relative abundance within 0–30, 30–60, 60–90 and >90 m depth strata differed between size classes suggesting that morphology changed when fish shifted their habitat as they grew older. Large C. artedi had lower δ13C and slightly higher δ15N, indicating greater reliance on pelagic prey resources (i.e. more or larger zooplankton, such as Mysis spp.), compared to small C. artedi, which relied slightly more on benthic prey. Gillraker shape and number have always been used as key diagnostic characters in coregonine taxonomy; based on the findings presented here, ontogenetic shifts should be accounted for in resulting classifications.