Based on specimens collected subtidally (∼10 m in depth) in Tomioka Bay, Japan, we describe the palaeonemertean Tubulanus tamias sp. nov., which differs from all its congeners in body coloration. In molecular phylogenetic analyses based on partial sequences of the nuclear 18S and 28S rRNA genes and histone H3, as well as the mitochondrial 16S rRNA and cytochrome c oxidase subunit I genes, among selected palaeonemerteans, T. tamias nested with part of the congeners in Tubulanus, while the genus as currently diagnosed appears to be non-monophyletic. Molecular cloning detected polymorphism in 28S rDNA sequences in a single individual of T. tamias, indicating incomplete concerted evolution of multiple copies. Tubulanus tamias is peculiar among tubulanids in having 9–10 pigment-cup eyes in the epidermis on either side of the head anterior to the cerebral sensory organs, and remarkably there are two types of eyes. The anterior 8–9 pairs of eyes, becoming larger from anterior to posterior, are completely embedded in the epidermis and proximally abutting the basement membrane; each pigment cup contains bundle of up to seven, rod-shaped structure that resemble a rhabdomeric photoreceptor cell. In contrast, the posterior-most pair of eyes, larger than most of the anterior ones, have an optical cavity filled with long cilia and opening to the exterior, thus appearing to have ciliary-type photoreceptor cells. The size and arrangement of the eyes indicate that the posterior-most pair of eyes are the remnant of the larval (or juvenile) eyes.