Avise, J.C. and F.J. Ayala, eds. In the Light of Evolution: Adaptation and Complex Design. National Academy Press: Washington, DC. 2007.
Cela Conde, C.J. and F.J. Ayala. Human Evolution. Trails from the Past. Oxford University Press: Oxford, UK. In press. 2007.
Ayala, F.J. Darwin y el Diseño Inteligente. Creacionismo, Cristianismo y Evolución. Alianza Editorial: Madrid, Spain, 231 pp. 2007.
Ayala, F.J. Darwin’s Gift to Science and Religion. Joseph Henry Press: Washington, DC, xi + 237 pp. 2007
Ayala, F.J. La Evolución de un Evolucionista. Escritos Seleccionados. University of Valencia: Valencia, Spain, 441 pp. 2006.
Ayala, F.J. Darwin and Intelligent Design. Fortress Press: Minneapolis, MN, xi + 116 pp. 2006.(フランシスコ・J・アヤラ『キリスト教は進化論と共存できるか?―ダーウィンと知的設計』 藤井清久訳、教文館、2008)
Ayala, F.J. and C.J. Cela Conde. La piedra que se volvió palabra. Las claves evolutivas de la humanidad. Alianza Editorial: Madrid, Spain. 184 pp. 2006
Hey, J., W.M. Fitch and F.J. Ayala, eds. Systematics and the Origin of Species. On Ernst Mayr’s 100th Anniversary. National Academies Press: Washington, DC. xiii + 367 pp. 2005
Wuketits, F.M. and F.J. Ayala, eds. Handbook of Evolution: The Evolution of Living Systems (Including Hominids), Volume 2. Wiley-VCH: Weinheim, Germany. 292 pp. 2005.
Ayala, F.J. Le Ragioni dell’ Evoluzione. Di Renzo Editore: Rome. 109 pp. 2005.
Le ragioni dell'evoluzione, Di Renzo Editore, Roma, 2005