Marine unarmored dinoflagellates of the family Kareniaceae are one of the most harmful blooming microalgae in Japan and adjacent waters. Harmful blooms of Karenia mikimotoi have continuously caused fisheries damages along the coast of western Japan, and in the autumn of 2021, a large cold-water bloom of Karenia selliformis caused mass mortality of marine benthic organisms in the Pacific coast of eastern Hokkaido. For unambiguous identification of kareniacean dinoflagellates in the K. selliformis, unialgal cultures of the Kareniaceae were established from samples of the 2021 bloom and after the bloom in 2022. Cell morphologies were observed by LM and SEM, and phylogenetic positions were inferred from LSU rDNA and ITS sequences. The 2021 bloom samples were dominated by K. selliformis, and other kareniaceans Karenia longicanalis, Karenia mikimotoi, Karlodinium sp., Takayama cf. acrotrocha, Takayama tuberculata, and Takayama sp. were also found. In the 2022 samples, K. cf. longicanalis, K. mikimotoi, K. cf. digitatum, Takayama sp. were found from Hokkaido waters, but K. selliformis was not detected. Kareniaceans observed in 2021 and 2022, K. mikimotoi and Takayama sp., might be endemic populations in Hokkaido. Cells of Karenia cf. longicanalis occurred in 2022 were similar to K. longicanalis in shape of cell and chloroplasts, but the anteriorly positioned nucleus was different from the central nucleus in K. longicanalis.