Original description as Fundulus punctatus:
- Günther, Albert C. L. G. 1866. "Catalogue of the Physostomi, containing the families Salmonidae, Percopsidae, Galaxidae, Mormyridae, Gymnarchidae, Esocidae, Umbridae, Scombresocidae, Cyprinodontidae, in the collection of the British Museum". Catalogue of the fishes in the British Museum. v. 6, pp. 1-368 (ffm04521)
Synonyms (2):
- Fundulus pachycephalus Günther, 1866, with type locality at Guatemala. Determiner: Lazara, 2001
- Profundulus balsanus Ahl, 1935, with type locality at Río Balsas system, Malinaltepec, Guerrero, Mexico. Determiner: Lazara, 2001
- Profundulus scapularis Fowler, 1936, with type locality at Río Bravo, Hoca, Guatemala. Determiner: Doadrio et al., 1999
Conservation: Profundulus punctatus is not evaluated by the international union for the conservation of nature in the iucn red list of threatened species.