Navajodactylus has been placed within the azhdarchidae pterosaurs, although so far no distinctive features of the group have been found in Navajodactylus. This however is down to the incomplete nature Navajodactylus fossils. Navajodactylus is not believed to be synonymous to any other known pterosaur because of the construction of the wing phalanx, loosely termed the hand. In the phalanx it is the connection for the extensor tendon that is different to other known fossils.
Navajodactylus has been found in only two locations but the geographical distance of these locations, New Mexico and Alberta, not only suggests a broad species range, but also indicates that Navajodactylus may have lived upon the fringes of the Western Interior Seaway, which submerged much of Cretaceous North America between New Mexico and Alberta. This in turn infers a piscivorous fish eating lifestyle for Navajodactylus.
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