A survey of threespine stickleback (Gasterosteus aculeatus L.) and juvenile Chinook salmon (Oncorhynchus tshawytscha (Walbaum)) from the lower Fraser River, British Columbia, Canada and adjacent marine waters was conducted for the presence of myxozoan parasites of the genus Ceratonova Atkinson, Foott, and Bartholomew, 2014 (Bivalvulida, Ceratomyxidae). Quantitative polymerase chain reaction (PCR; small subunit ribosomal RNA gene) combined with conventional PCR and sequencing (ribosomal internal transcribed spacer region 1) detected Ceratonova gasterostea Atkinson, Foott, and Bartholomew, 2014 in 89 of 269 (33.1%) sticklebacks from the Fraser River and in 1 of 51 (2%) from Howe Sound. In contrast, Ceratonova shasta (Atkinson, Foott, and Bartholomew, 2014) was detected in 2 of 26 (7.7%) Chinook salmon from the Fraser River. Reciprocal infections were not detected. Light microscopic examination of the stickleback intestine revealed the presence of an intense infection with large numbers of pseudoplasmodia which interacted with enterocytes through pseudopodia-like projections. Myxospores with characteristic elongate valve cells were visible within mature pseudoplasmodia and free in the intestinal lumen. This is the first report of C. gasterostea in Canada.