Rhodeus atremius, an endemic bitterling fish from Japan, comprises two endangered subspecies: R. a. atremius and R. a. suigensis. The latter subspecies, designated as a Nationally Endangered Species of Wild Fauna and Flora by the Ministry of Environment of Japan, is noted for drastic declines and the extinction of local populations through habitat deterioration. Despite their strong phenotypic resemblance, these two subspecies are much diverged in DNA, each forming a distinct evolutionary lineage. Nevertheless, these two subspecies were clumped into a single subspecies, R. smithii smithii, in a newly published fish encyclopedia, which will lead to R. a. suigensis being dropped from the list of Nationally Endangered Species. This paper critically reviews the validity of this new taxonomic arrangement of R. atremius, including R. a. suigensis, based on phylogenetic systematics. Its potential risk against the conservation management of R. a. suigensis is specifically discussed.