The type specimen of Kinkonychelys rogersi, n. gen. et sp., is the first turtle skull to be described from the pre-Holocene fossil record of Madagascar. This specimen, a nearly complete cranium, along with several referred specimens (a series of maxillae and a partial lower jaw), was recovered from the Maastrichtian Maevarano Formation in the Mahajanga Basin of northwestern Madagascar. A braincase with the diagnostic characters of Kinkonychelys, but differing in the position of the jaw articulation, formation of the foramen nervi facialis, and a number of other characters, was found in the same rock unit and is provisionally identified as belonging to Kinkonychelys sp., a presumed distinct, but closely related species, too incomplete to be diagnosed at present.

Kinkonychelys is a bothremydid because it has the diagnostic characters of an exoccipital-quadrate contact and a fully enclosed incisura columellae auris (Gaffney et al., 2006). Kinkonychelys belongs to the tribe Kurmademydini, previously known to include only Sankuchemys and Kurmademys from the Late Cretaceous of India, because it has a deep fossa pterygoidea, a foramen stapediotemporale facing dorsally, a jugal not retracted from the orbit, a deep fossa precolumellaris, and a large, wide antrum postoticum. Kinkonychelys rogersi and Kinkonychelys sp. both possess a unique form of the overlapping fossa pterygoidea.

A cladistic analysis of Kinkonychelys reveals that it is nested within the tribe Kurmademydini of Gaffney et al. (2006) and is related to the other taxa in the tribe as follows: (Sankuchemys (Kinkonychelys Kurmademys)). The discovery of a Malagasy bothremydid of Maastrichtian age that is nested within the Indian members of the Kurmademydini supports the hypothesis of a connection between Madagascar and the Indian subcontinent that persisted into the late stages of the Late Cretaceous.