A novel brown algal genus and species Setoutiphycus delamareoides (Ectocarpales sensu lato) is described from the Seto Inland Sea, Japan. The species is similar to Delamarea attenuata in gross morphology and anatomy, but distinctive in having longer thalli with rare branching, shorter cortical cells, and occurrence of branches at the tip of plurilocular zoidangia. Erect thalli were epilithic, solitary or caespitose, filiform, simple or rarely branched, attenuated towards the base, blunt at the tip, with uneven surface, yellowish brown in color, up to about 15 cm in height and 2 mm in diameter, parenchymatous, solid when young and later becoming hollow, composed of 1–2 layers of large colorless inner cells, subcortical cells, barrel-shaped large cortical cells of up to 100 µm in height and up to 60 µm in diameter, and phaeophycean hairs. Plurilocular and unilocular zoidangia developed on the same thallus, the former conical to lanceolate, sometimes branched at the tip and projected from the cortical cells, and the latter ovate. Each cell contained many discoidal chloroplasts with projected pyrenoids. In the molecular phylogeny using concatenated DNA sequences of mitochondrial cox1, cox3 and chloroplast atpB, psaA, psbA and rbcL genes, the novel alga nested in the clade composed of ectocarpalean genera of diffuse growth, with parenchymatous thalli with multiple chloroplasts, but was distinctive. Therefore, we propose the establishment of a new genus and species Setoutiphycus delamareoides gen. & sp. nov. for the novel alga, and provisionally place it in Chordariaceae, Ectocarpales sensu lato. As to the biogeography, the Seto Inland Sea repeatedly dried by sea level regression during the glacial periods and the present sea level has recovered after the LGM of ca. 10,000 years ago. Therefore, it is unlikely that the evolution of the genus and species occurred within this area, and its isolated distribution may be explained as a remnant population that survived in the refugia in southern Japan during LGM. It is possible that the species also has a broader distributional range, at least in Japan, such as northern Honshu, but if not, the species can be endangered due to the raise of seawater temperature in the area by global climate change, because the Seto Inland Sea is enclosed at its northern end, so the population cannot spread to colder more northern coasts.