The first fossils, among them the holotype PVL 2571, a thigh bone, were discovered during the late 1960s by José Bonaparte in the Lagarcito Formation, situated in the San Luis Province of Argentina, and dating from the Albian.

The genus was subsequently reported in Chile from the Quebrada La Carreta locality, in the Sierra da Candeleros, Segunda Región de Antofagsta, but this turned out to be erroneous; the fossils belong another pterosaur, the dsungaripterid Domeykodactylus ceciliae.

Pterodaustro has about a thousand bristle-like modified teeth in its lower jaws that might have been used to strain crustaceans, plankton, algae, and other small creatures from the water.

Pterodaustro probably strained food with its tooth comb, a method called "filter feeding", also practised by modern flamingos.

[14] A study of the growth stages of Pterodaustro concluded that juveniles grew relatively fast in their first two years, attaining about half of the adult size.

Even with the pterosaurian quadrupedal launching mechanism, it would have required frantic and fairly-low angled take-offs possible only in open areas, much like modern geese and swans.

However, from 1996 cladistic studies by Alexander Kellner and David Unwin have shown a position within the family Ctenochasmatidae, together with other filter feeders.

[11] In 2018, a topology by Longrich, Martill and Andres recovered Pterodaustro within the family Ctenochasmatidae, more precisely within the tribe called Pterodaustrini, in a more basal position than Beipiaopterus and Gegepterus.

[21] Ctenochasma Pterodaustro Beipiaopterus Gegepterus Kepodactylus Moganopterus Feilongus Ardeadactylus Elanodactylus Huanhepterus Plataleorhynchus Gnathosaurus