It was originally described as Monopterus indicus by K. C. Eapen in 1963, but another fish with the same scientific name, the Bombay swamp eel had already been described 2 years prior. Due to this causing a homonym the species had to be renamed but due to the lack of specimens, it was tentatively referred to as Monopterus "indicus". It was later redescribed as Monopterus eapeni in 1991. A 2020 study found M. eapeni to form a clade with two other troglobitic species from the Western Ghats and one fossorial species from Northeast India, leading it to be reclassified in the new genus Rakthamichthys, lifting the homonym problem and allowing the original specific epithet of indicus to be revived.