Cellana nigrolineata is amongst the most common and largest patellogastropod limpets in Japan, and has two color morphs. Analyses of anatomical and morphological characters, shell structure, and mitochondrial COI data (658bp) of these color morphs suggested that they represent intraspecific genetic variation. Molecular analysis demonstrated that the species can be subdivided into three genetically distinct groups: (Clade 1) Honshu, Shikoku to Eastern Kyushu, (Clade 2) Western Kyushu and (Clade 3) Southern Kyushu. Clade 1 and Clade 2 + 3 are distributed on the coastlines adjacent to two warm-water currents, the Kuroshio and Tsushima Currents, respectively. The southern population (Clade 3) is currently isolated by inhospitable sandy shores. The subdivision of these groups likely dates from the glacial period of Plio-Pleistocene time.