Phylogenetic and morphological reinvestigation of Chondrus verrucosus Mikami was conducted in the Pacific coast of southeastern Honshu, Japan, including the holotype specimen and samples near the type locality. Two entities were recognized by phylogenetic analyses of plastid rbcL and nuclear EF2 sequences. In morphological analyses, the two entities were distinguished by: (i) thallus size and form, and (ii) cell shape of the medullary layer surrounding young carposporangia: one has larger thalli, is regularly canaliculated, with linear medullary cells (large-type); the other is smaller, canaliculated with crispation and has roundish medullary cells (small-type). The large-type was common in southern to eastern Boso Peninsula including near the type locality; the small-type was typical in the southwest Boso Peninsula and Sagami Bay. The large-type was shown to be equivalent to C. verrucosus by examination of the holotype specimen. The small-type is described as a new species, C. retortus Matsumoto et Shimada.