Original description as Heros motaguensis:
- Günther, Albert C. L. G. 1867. "On the fishes of the states of Central America, founded upon specimens collected in fresh and marine waters of various parts of that country by Messrs. Salvin and Godman and Capt. J. M. Dow". Proceedings of the Zoological Society of London. 1866:600-604 (crc00014)
Conservation: Parachromis motaguensis is evaluated by the international union for the conservation of nature in the iucn red list of threatened species as (LC) least concern (2019).