The first "Nyctosaurus" fossils were described in 1876 by Othniel Charles Marsh, based on fragmentary material, holotype YPM 1178, from the Smoky Hill River site in Kansas. Marsh referred the specimen to a species of his new genus "Pteranodon", as "Pteranodon gracilis". Later that year, Marsh reclassified the species in its own genus, which he named "Nyctosaurus", meaning "night lizard" or "bat lizard", in reference to the wing structure somewhat paralleling those of bats. In 1881, Marsh incorrectly assumed the name was preoccupied and changed it into "Nyctodactylus", which thus is now a junior synonym. In 1902, Samuel Wendell Williston described the most complete skeleton then known (P 25026) discovered in 1901 by H. T. Martin. In 1903, Williston named a second species, "N. leptodactylus", but this is today considered identical to "N. gracilis".