Individuals of a deep-sea snailfish, Careproctus trachysoma, endemic to the Japan Sea have been classified into the lighter and darker color morphotypes, which are sympatrically distributed. These morphotypes have only been described qualitatively, with individuals that could not be classified as either morphotype. Therefore, in this study, we quantitatively evaluated individuals of this species using a colorimeter. Based on principal component analysis, all examined individuals were classified into two groups containing all typical individuals of the two original color morphotypes. We redefined these groups as "Red" and "Black" morphotypes. Stomach contents, sex, body length, and sampling depth did not clarify the color differences between Red and Black individuals. No genetic differences were detected between morphotypes using microsatellites, although the frequency of two mitochondrial DNA (mtDNA) groups, SOJ1 and SOJ2, was found to be significantly different. Individuals with SOJ1-type mtDNAs, which are thought to have migrated into the Japan Sea more recently than those with SOJ2-type mtDNA, showed body coloration similar to that of the Pacific species, C. pellucidus. Although further studies using more specimens are required to confirm these findings, our results indicate that C. trachysoma body color is related to mtDNA lineages.