Thiamine (vitamin B1) deficiency is a global concern affecting wildlife, livestock, and humans. In Great Lakes salmonines, thiamine deficiency causes embryo mortality and is an impediment to restoration of native lake trout (Salvelinus namaycush) stocks. Thiamine deficiency in fish may result from a diet of prey with high levels of thiaminase I. The discoveries that the bacterial species Paenibacillus thiaminolyticus produces thiaminase I, is found in viscera of thiaminase-containing prey fish, and causes mortality when fed to lake trout in the laboratory provided circumstantial evidence implicating P. thiaminolyticus. This study quantified the contribution of P. thiaminolyticus to the total thiaminase I activity in multiple trophic levels of Great Lakes food webs. Unexpectedly, no relationship between thiaminase activity and either the amount of P. thiaminolyticus thiaminase I protein or the abundance of P. thiaminolyticus cells was found. These results demonstrate that P. thiaminolyticus is not the primary source of thiaminase activity affecting Great Lakes salmonines and calls into question the long-standing assumption that P. thiaminolyticus is the source of thiaminase in other wild and domestic animals.