分類体系に従えば、エナンティオルニス類は真鳥類(あるいは“真鳥形類”)の姉妹群であり、真鳥類とあわせて鳥胸類という系統群を構成する。これまで、系統分類の研究者はエナンティオルニス類を単系統の分類群として設立するのに反対してきた[23]。しかし近年の系統学的研究によれば、エナンティオルニス類は真鳥類に近縁ではあるが独立した単系統群であると結論づけている。ただし、Clarke and Norell (2002)によればエナンティオルニス類の固有派生形質はわずか4つに限られる[2]。現在もエナンティオルニス類の研究は発展途上であるため、本項目で提示した分類や分岐図はあくまでも暫定的なものである。近い将来、保存状態のよい化石標本の発見によって、分類と系統関係の解釈は大きく変わるかもしれない。
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