The fossilized remains of Rahonavis were first recovered from the Maevarano Formation in Madagascar in 1995 by a joint expedition of SUNY and the University of Antananarivo, near the village of Berivotra.

Although former character can vary in species of the same genus, in individual vertebrae of the same animal, and ontogenetically, the distance in space and time suggests that whatever this specimen may be, it does not belong into Rahonavis.

The presence of quill knobs on its ulna (forearm bone) led initially to its inclusion as an avialan; however, the rest of the skeleton is rather typically dromaeosaurid in its attributes.

[9] Beginning in the early 2000s, a consensus emerged among most theropod researchers that Rahonavis was more closely related to deinonychosaurs than to avialans, and specifically was a member of the South American dromaeosaurid clade Unenlagiinae.

[14] The analysis of Hartman et al. (2019) "strongly rejected" the supposed avialan position of Rahonavis, finding its placement in Unenlagiinae better supported as it takes 10 less steps.

[8] Although numerous artists' reconstructions of Rahonavis show it in flight, it is not clear that it could fly; there has even been some doubt that the forearm material, which includes the quill knobs, belongs with the rest of the skeleton.

Some researchers have suggested that Rahonavis represents a chimera consisting of the forelimb of a bird conflated with the skeleton of a dromaeosaurid, and consider Rahona as described a nomen dubium.

However, many other scientists, including the original describers of Rahonavis, maintain that its remains belong to a single animal, citing the close proximity of the wing bones to the rest of the skeleton.