Makovicky and colleagues consider "Rahonavis" to be closely related to the South American dromaeosaurids "Unenlagia" and "Buitreraptor", and thus a member of the subfamily Unenlagiinae. Norell and colleagues (2006) also found "Rahonavis" to lie within the Unenlagiinae, as the sister taxon to "Unenlagia" itself. A 2007 study by Turner and colleagues again found it to be closely related to "Unenlagia". However, studies published since 2009 that have found many traditional "dromaeosaurids", including the unenlagiines, closer to Avialae than to dromaeosaurines. A cladistic analysis recovered "Rahonavis" as a probable relative of "Jeholornis" and "Jixiangornis".
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