Lyons, John & S. Navarro-Pérez. 1990. "Fishes of the Sierra de Manantlan, West-Central Mexico". The Southwestern Naturalist. 35(1):32-46 (ffm00631) (abstract)
Lyons, John. 1991. "Fishes from the land of the trucha de tierra caliente". Freshwater and Marine Aquarium (FAMA). 14(7):127-136 (ffm12033)
Lyons, John & Sonia Navarro Pérez, Philip A. Cochran, Eduardo Santana, Manuel Guzmán-Arroyo. 1995. "Index of biotic integrity based on fish assemblages for the conservation of streams and rivers in west-central Mexico". Conservation Biology. 9(2):569-584 (ffm01176) (abstract)
Lyons, John & O.J. Polaco, P.A. Cochran. 1996. "Morphological variation among the Mexican lampreys (Petromyzontidae: Lampetra: subgenus Tetrapleurodon)". Southwestern Naturalist. 41(4):365-374 (ffm00914)
Lyons, John & Georgina González-Hernández,Eduardo Soto-Galera,Manuel Guzmán-Arroyo. 1998. "Decline of freshwater fishes and fisheries in selected drainages of west-central Mexico". Environmental Biology of Fishes. 10(4):10-18. DOI: 10.1577/1548-8446%281998%29023<0010%3ADOFFAF>2.0.CO%3B2 (ffm01009) (abstract)
Lyons, John. 1999. "The darter Goodeids, Genus Allodontichthys". Livebearers - Journal of the American Livebearer Association. 158/159:14-18 (ffm00287)
Lyons, John & Norman Mercado-Silva. 2000. "Peces dulceacuicolas mexicanos: Allodontichthys (Goodeidae)". Zoología Informa. (43):3–16 (ffm00994)
Lyons, John. 2002. "De grondbaars Goodeiden, het geslacht Allodontichthys". Poecilia Nieuws. 19(5):91-95 (ffm00650)
Lyons, John. 2002. "Het natuurlijk verspreidingsgebied van de luipaard Goodeide Xenotaenia resolanae". Poecilia Nieuws. 19(4):61-73 (ffm00647)
Lyons, John & N. Mercado-Silva. 2004. "Notropis calabazas (Teleostei; Cyprinidae): New Species from the Río Pánuco Basin of Central México". Copeia. 2004(4):868–875 (ffm00148)
Lyons, John. 2013. "Schutzstatus und Entwicklungstrends von Populationen Mexikanischer Hochlandkärpflinge in der Natur". Beiträge zur Biologie und zum Artenschutz der Hoch land kärpflinge. 61-112 (ffm00757) (abstract)
Lyons, John & Kyle R. Piller, Juan Miguel Artigas-Azas, Omar Dominguez-Dominguez, Pablo Gesundheit, Michael Köck, Martina Medina-Nava, Norman Mercado-Silva, Arely Ramírez García, Kearstin M. Findley. 2019. "Distribution and current conservation status of the Mexican Goodeidae (Actinopterygii, Cyprinodontiformes)". Zookeys. (885):115-158. DOI: 10.3897/zookeys.885.38152 (ffm00903) (abstract)