Adaptation to an aquatic habitat results in dramatic changes in tetrapod limb morphology as limbs take on the roles of propulsion and steering and lose their weight-bearing function. Changes include enclosure of the limb in a soft-tissue flipper and proportional lengthening of the distal limb, often accomplished through the addition of skeletal elements (hyperphalangy). The flipper structure itself and changes to the developmental architecture permitting hyperphalangy are hypothesized to increase observed limb variation, based on a cetacean model. These hypotheses are examined in the ichthyosaurs Stenopterygius and Mixosaurus. Hyperphalangy combined with high levels of variation in phalangeal counts were observed in both genera. The amount of variation was not proportional to the number of phalanges in a digit, but was related to functional digit length. In addition, qualitative variants were catalogued in both genera. Polyphalangy, phalangeal fusion, and additional ossifications in the zeugopodial row were not observed in Mixosaurus, but were common in Stenopterygius, even though both genera exhibited a similar degree of hyperphalangy. These results suggest that while the flipper structure and processes resulting in hyperphalangy may increase observed variation in phalangeal counts, these factors are unlikely to be causing high levels of qualitative variation in ichthyosaurs. Patterns of variation in ichthyosaur limbs, and thus variability, are unique to species but can change over evolutionary time. J. Exp. Zool. (Mol. Dev. Evol.) 318B:545–554, 2012. © 2012 Wiley Periodicals, Inc.