Previous studies have recorded Spironucleus torosus Poynton et Morrison, 1990 from several species of gadoid fishes, including the only freshwater gadoid, the burbot Lota lota (L.). Two morphologically different isolates of S. torosus have been described (elongate and pyriform). Both have been found in saltwater, while only the elongate has been found in freshwater. To address the conspecificity of the two morphs of S. torosus, and to identify the source of S. torosus in burbot in Norway, we have sequenced the small subunit ribosomal RNA (SSU rRNA) gene from 43 isolates of S. torosus from six species of gadoid fishes sampled at 15 localities in Norway, Sweden and the Baltic Sea. Phylogenetic analyses of the SSU rRNA gene sequence data recovered two major clades, one containing mainly isolates from burbot, while the other contained isolates from marine gadoid fishes only. The genetic distance (based on 25 nucleotide substitutions in 789 base pairs) separating the two assemblages was not large enough to consider the two groups separate species. Spironucleus torosus isolated from burbot displayed limited genetic variation in the small subunit ribosomal RNA (SSU rRNA) gene along the post-Pleistocene migration route of its host. The present study is the first report of S. torosus in tusk Brosme brosme (Ascanius), whiting Merlangius merlangus (L.), and fourbeard rockling Enchelyopus cimbrius (L.).