Principal component and discriminant function analyses of morphological variation between whitefish populations from the Canadian Maritime Provinces and the State of Maine, USA, clearly distinguished the Acadian whitefish, Coregonus huntsmani, from the lake whitefish species complex, Coregonus clupeaformis. Ten meristic and 44 morphometric characters were examined and the species were best discriminated by number of vertebrae (>97% separation) and mouth shape. Acadian whitefish had a terminal mouth and 64–67 [Formula: see text] vertebrae, while lake whitefish had a subterminal mouth and 58–64 [Formula: see text] vertebrae. Acadian whitefish were also characterized by having more lateral line scales (88–100, [Formula: see text] than lake whitefish (63–95, [Formula: see text], a shorter adipose to caudal fin length, a smaller adipose fin, and a longer pelvic axillary process than lake whitefish. Considerable morphological variation was found between lake whitefish populations examined although there was no morphological basis to recognize any lake whitefish population as taxonomically distinct. The Acadian whitefish has morphological characteristics of both subgenera Leucichthys and Coregonus; it could be important for understanding the evolution of coregonine fishes and its imminent extinction would represent a serious loss of genetic diversity.