Original description as Gobius microdon:
- Gilbert, Carter R.. 1892. "Descriptions of thirty-four new species of fishes collected in 1888 and 1889, principally among the Santa Barbara Islands and in the Gulf of California". Scientific results of explorations by the U. S. Fish Commission steamer Albatross. v. 14(n. 880), pp. 539-566 (ffm00445)
- Gobionellus mystax Ginsburg, 1953, with type locality at Laguna de Mexcalititan, Territory of Tepic [now the state of Nayarit], Mexico. Determiner: Pezold, 2004
Conservation: Gobionellus microdon is evaluated by the international union for the conservation of nature in the iucn red list of threatened species as (LC) least concern (2010).