Leguat's 1708 map of pristine Rodrigues; his settlement can be seen to the northeast. Rodrigues solitaires are sprinkled all over the map
The French explorer François Leguat was the first to refer to the bird as the "solitaire" (referring to its solitary habits), but it has been suggested that he borrowed the name from a 1689 tract by Marquis Henri Duquesne, his sponsor, mentioning the Réunion solitaire. The bird was first scientifically named in 1789 as a species of dodo (Didus solitarius, based on Leguat's description) by the German naturalist Johann Friedrich Gmelin in the thirteenth edition of Systema Naturae. The English naturalists Hugh Edwin Strickland and Alexander Gordon Melville suggested the common descent of the Rodrigues solitaire and the dodo in 1848. They dissected the only known dodo specimen with soft tissue, comparing it with the few Rodrigues solitaire remains then available.
Strickland stated that, although not identical, these birds shared many distinguishing features in the leg bones otherwise only known in pigeons. The fact that the Rodrigues solitaire laid only one egg, fed on fruits, was monogamous and cared for its nestlings also supported this relationship. Strickland recognised its generic distinction and named the new genus Pezophaps, from ancient Greek pezos (πεζός ‘pedestrian’) and phaps (φάψ ‘pigeon’). The differences between the sexes of the bird were so large that Strickland thought they belonged to two species, naming the smaller female bird Pezophaps minor. Later study of skeletal features by the English ornithologists (and brothers) Alfred and Edward Newton indicated that the solitaire was morphologically intermediate between the dodo and ordinary pigeons, but differed from them in its unique carpal knob.
The term "solitaire" has also been used for other species with solitary habits, such as the Réunion ibis. Some scientists believed that Réunion was home not only to a white dodo, but also to a white bird similar to the Rodrigues solitaire, both of which are now believed to be misinterpretations of old reports of the ibis. An atypical 17th-century description of a dodo and bones found on Rodrigues, now known to have belonged to the Rodrigues solitaire, led the British taxidermist Abraham Dee Bartlett to name a new species, Didus nazarenus; it is now a junior synonym of this species.
For many years the dodo and the Rodrigues solitaire were placed in a family of their own, the Raphidae (formerly Dididae), because their exact relationships with other pigeons were unresolved. Each was also placed in a monotypic family (Raphidae and Pezophapidae, respectively), as it was thought that they had evolved their similarities independently. Osteological and DNA analysis has since led to the dissolution of the family Raphidae, and the dodo and solitaire are now placed in their own subfamily, Raphinae, within the family Columbidae.
In 2002, American geneticist Beth Shapiro and colleagues analysed the DNA of the dodo and the Rodrigues solitaire for the first time. Comparison of mitochondrial cytochrome b and 12S rRNA sequences isolated from the femur of a Rodrigues solitaire and the tarsal of a dodo confirmed their close relationship and their placement within the Columbidae. The genetic evidence was interpreted as showing the Southeast Asian Nicobar pigeon (Caloenas nicobarica) to be their closest living relative, followed by the crowned pigeons (Goura) of New Guinea, and the superficially dodo-like tooth-billed pigeon (Didunculus strigirostris) from Samoa. This clade consists of generally ground-dwelling island endemic pigeons. The following cladogram shows the closest relationships of the dodo and the Rodrigues solitaire within Columbidae, based on Shapiro et al., 2002:
A similar cladogram was published in 2007, inverting the placement of Goura and Dicunculus and including the pheasant pigeon (Otidiphaps nobilis) and the thick-billed ground pigeon (Trugon terrestris) at the base of the clade. Based on behavioural and morphological evidence, Jolyon C. Parish proposed that the dodo and Rodrigues solitaire should be placed in the Gourinae subfamily along with the Groura pigeons and others, in agreement with the genetic evidence. In 2014, DNA of the only known specimen of the recently extinct spotted green pigeon (Caloenas maculata) was analysed, and it was found to be a close relative of the Nicobar pigeon, and thus also the dodo and Rodrigues solitaire.
The 2002 study indicated that the ancestors of the Rodrigues solitaire and the dodo diverged around the Paleogene-Neogene boundary. The Mascarene Islands (Mauritius, Réunion, and Rodrigues), are of volcanic origin and are less than 10 million years old. Therefore, the ancestors of both birds probably remained capable of flight for a considerable time after the separation of their lineage. The Nicobar and spotted green pigeon were placed at the base of a lineage leading to the Raphinae, which indicates the flightless raphines had ancestors that were able to fly, were semi-terrestrial, and inhabited islands. This in turn supports the hypothesis that the ancestors of those birds reached the Mascarene islands by island hopping from South Asia. The lack of mammalian herbivores competing for resources on these islands allowed the solitaire and the dodo to attain very large sizes. The dodo lost the ability to fly owing to the lack of mammalian predators on Mauritius. Another large, flightless pigeon, the Viti Levu giant pigeon (Natunaornis gigoura), was described in 2001 from subfossil material from Fiji. It was only slightly smaller than the Rodrigues solitaire and the dodo, and it too is thought to have been related to the crowned pigeons.