Specimens of Sphaerotrichia in Japan can be classified into two morphotypes based on mode of branching and anatomy: 1) specimens having an obvious (traceable) main axis associated with more first-order branches, and the distance between the branches is relatively constant; 2) specimens that branches more or less divaricately and the distance between branches tends to be shorter in the distal portion. Molecular analyses of North Atlantic and North Pacific Sphaerotrichia using ribo-somal RNA (ITS1-5.8S-ITS2 and IGS regions between 26S and 5S rDNA) and Rubisco (almost complete rbcL gene and the spacer between rbcL and rbcS) gene sequences revealed that there are two major genetic groups (i.e. Group-1 and Group-2), whereas the sequence length variation in ITS1 suggested subdivisions of Group-2 into two subgroups (Group-2Atlantic and Group-2Pacific). Specimens belonging to Group-1 were generally epilithic, and morphologically corresponded to Sphaerotrichia firma (Gepp) A. Zinova. Specimens belonging to Group-2 were epiphytic or epilithic and morphologically corresponded to S. divaricata (C. Ag.) Kylin.