López-Fernández, Hernán & D.C. Taphorn. 2004. "Geophagus abalios, G. dicrozoster and G. winemilleri (Perciformes: Cichlidae), three new species from Venezuela". Zootaxa. 439:1-27 (crc00077) (abstract)
López-Fernández, Hernán & Rodney L. Honeycutt, Kirk O. Winemiller. 2005. "Molecular phylogeny and evidence for an adaptative radiation of geophagine cichlids from South America (Perciformes: Labroidei)". Molecular Phylogenetics and Evolution. 34(1):227-244 (crc02372) (abstract)
López-Fernández, Hernán & Rodney L. Honeycutt, Melanie L.J. Stiassny, Kirk O. Winemiller. 2005. "Morphology, molecules, and character congruence in the phylogeny of South American geophagine cichlids (Perciformes, Labroidei)". Zoologica Scripta. 34(6):627-651. DOI: 10.1111/j.1463-6409.2005.00209 (crc02376) (abstract)
López-Fernández, Hernán. 2006. "Geophaginae: Earth eating is not the whole story.". Buntbarsche Bulletin. (233):8-14 (crc03326) (abstract)
López-Fernández, Hernán & Donald C. Taphorn, Baechle, Sven O. Kullander. 2006. "Two new species of Guianacara from the Guiana Shield of eastern Venezuela (Perciformes: Cichlidae)". Copeia. 2006(3):384–395. DOI: 10.1643/0045-8511(2006)2006[384:TNSOGF]2.0.CO;2 (crc01324) (abstract)
López-Fernández, Hernán & K.O. Winemiller, R.L. Honeycutt. 2010. "Multilocus phylogeny and rapid radiations in Neotropical cichlid fishes (Perciformes: Cichlidae: Cichlinae)". Molecular Phylogenetics and Evolution. 55(3):1070–1086. DOI: 10.1016/j.ympev.2010.02.020 (crc02456) (abstract)
López-Fernández, Hernán & K.O. Winemiller, C. Montaña, R.L. Honeycutt. 2012. "Diet-morphology correlations in the radiation of South American Geophagine cichlids (Perciformes: Cichlidae: Cichlinae)". Plos One. 7(4):e33997. DOI: 10.1371/journal.pone.0033997 (crc05250) (abstract)
López-Fernández, Hernán & Donald C. Taphorn, Elford A. Liverpool. 2012. "Phylogenetic diagnosis and expanded description of the genus Mazarunia Kullander, 1990 (Teleostei: Cichlidae) from the upper Mazaruni River, Guyana, with description of two new species". Neotropical Ichthyology. 10(3):465-486 (crc04572) (abstract)
López-Fernández, Hernán & J.H. Arbour, K.O. Winemiller, R.L. Honeycutt. 2013. "Testing for ancient adaptive radiations in neotropical cichlid fishes". Evolution. 67(5):1321–1337. DOI: 10.1111/evo.12038 (crc05261) (abstract)
López-Fernández, Hernán & J. Arbour, S. Willis, C. Watkins, R.L. Honeycutt, K.O. Winemiller. 2014. "Morphology and Efficiency of a Specialized Foraging Behavior, Sediment Sifting, in Neotropical Cichlid Fishes". Plos One. 9(3):e89832(1-9). DOI: 10.1371/journal.pone.0089832 (crc06132) (abstract)
López-Fernández, Hernán. 2014. "The found fish of the lost world". Practical Fishkeeping. 2014(2):28-33 (crc05971)
López-Fernández, Hernán. 2021. "Neotropical riverine cichlids: Adaptive radiation and macroevolution at continental scales". In: M.E. Abate & D.L.G. Noakes (Eds.) The Behavior, Ecology and Evolution of Cichlid Fishes: A Contemporary Modern Synthesis. Springer Academic. 135-173. DOI: 10.1007/978-94-024-2080-7_5 (crc11678) (abstract)