Original description as Heros trimaculatus:
- 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, pp. 600-604 (ffm00014)
- Cichlasoma mojarra Meek, 1904, with type locality at San Gerónimo, Oaxaca, Mexico. Determiner: Miller, 1966
- Cichlasoma centrale Meek, 1906, with type locality at Caballo Blanco, Guatemala. Determiner: Miller, 1966
- Cichlasoma tenue Meek, 1906, with type locality at Achotal, Veracruz, Mexico (likely in error). Determiner: Miller, 1976
- Cichlasoma gordonsmithi Fowler, 1936, with type locality at Small lake at Moco, at foot of volcano of Atitlan, Guatemala, elevation 3050 ft. Determiner: Miller, 1966
- Cichlasoma cajali Alvarez & Gutierrez, 1953, with type locality at Laguna de Coyuca, Acapulco, Mexico. Determiner: Miller, 1966
Conservation: Amphilophus trimaculatus is evaluated by the international union for the conservation of nature in the iucn red list of threatened species as (LC) least concern (2018). Given their large distribution and low human industrial activity in the distribution area of Amphilophus trimaculatus, it can be considered safe at present time.