A link was previously established between the Cayuga syndrome, a condition causing 100% mortality in larval landlocked Atlantic salmon, Salmo salar, in several of New York's Finger Lakes, and a maternal diet of alewife, Alosa pseudoharengus, a non-native thiaminase-rich Clupeid fish. We evaluated salmon larvae viability relative to maternal thiamin status, and investigated the putative link of the Cayuga syndrome to an alewife diet in fish from the geographic regions outside the Finger Lakes/lower Great Lakes watersheds. We identified Cayuga syndrome in Atlantic salmon from Otsego Lake in the Susquehanna River watershed and from Green Pond in New York's Adirondack Mountains. In both systems alewife represent the major component of the diet for the salmon. Thiamin levels in the maternal blood of Otsego salmon with syndrome-negative progeny were three- to four-fold greater than those Otsego females whose progeny exhibited 100% mortality. Thiamin levels in eggs and larvae were directly related to thiamin levels in maternal blood in both syndrome-positive and syndrome-negative stocks. Thiamin bath treatments of syndrome-afflicted larvae eliminated mortality regardless of their lake stock of origin. Maternal blood levels of approximately 0.31 nmol thiamin pyrophosphate/g or 0.44 nmol total thiamin/g appear necessary to achieve egg threshold levels of approximately 0.8 and 1.1 nmol/g unphosphorylated and total thiamin, respectively; these egg thiamin levels should prevent significant syndrome-related mortality in landlocked Atlantic salmon larvae. These results confirm the role of thiamin in the etiology of the Cayuga syndrome and support the dietary link of this naturally occurring thiamin deficiency to the thiaminase-rich alewife.