The ophthalmosaurid Caypullisaurus from the Late Jurassic–Early Cretaceous of the Neuquén Basin, Argentina, is redescribed based on new information from recent discoveries. Cladistic analysis of Caypullisaurus, based on previous ichthyopterygian data sets and using NONA, yielded two most parsimonious trees. Two clades are recognized within the Ophthalmosauridae. Caypullisaurus is found to be nested with Brachypterygius and Platypterygius. Simultaneous, unconstrained analysis, using unambiguous character optimization, is suggested as the best way to analyze data sets with large amounts of missing data.