Maupas studied the life-history and reproduction of many species using innovative culture techniques. He examined conjugation in ciliates and established that senescence and death occurred in ciliates, contrary to the view of August Weismann and others that they were immortal, following sexual reproduction. Maupas did not agree that the main value of sexual reproduction was in the maintenance of variability. He argued that it helped in rejuvenating the nucleus of one of the two conjugants. He also suggested that there were sexes or mating types in rotifers, including parthenogenetic females. Maupas also studied nematodes and first described Rhabditis elegans (now Caenorhabditis elegans) in 1900 and isolated it from soil in Algeria. His culture techniques enabled the species to become one of the most widely studied model organisms. He noted that nematodes had a five stage development with the fifth being the adult stage. The annelid genus Maupasia is named after him, as is the ascarid genus Maupasiella  (synonym Maupasina Seurat, 1913).