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Acknowledgements: This work was funded by a grant from the Australian Research Council (ARC) awarded to JH (DE120100107). M.B. was supported in this research by an ARC future fellowship (FT0991741). G.F. wishes to acknowledge the National Geography Society, as well as the Easterbrook Distinguished Scientist Award (from the Division of Quaternary Geology and Geomorphology Division of the Geological Society of America), for funding sample collecting trips in Madagascar. B.D.’s work received support from the Ministry of University and Research (Young researchers “Rita Levi Montalcini”). KD’s collections were made possible with funding from the National Science Foundation Graduate Research Fellowship Program, the P.E.O. Scholar Award, the Yale Institute of Biospheric Studies, the Yale MacMillan Center for International and Area Studies and the Yale Council on Archaeological Studies. Research permissions were granted by the Ministère de l’Enseignement Supérieur et de la Recherche Scientifique, Autorisation Numéro 128/13-MESupReS/SG/DGRP and by the Centre de Documentation et de Recherche sur l’Art et les Traditions Orales Malgaches (CEDRATOM), under the auspices of the Memorandum of Understanding between the University of Toliara, under the direction of Dr. Barthélémy Manjakahery, Director of the CEDRATOM, and Yale University, under the direction of Dr. Roderick McIntosh, Professor of Anthropology. Research permissions were also granted to Gifford Miller (University of Colorado, Boulder) by Director Jean-Aimé Rakotoarisoa of L’Institut de Civilisations – Musée d’Art et d’Archéologie de l’Université d’Antananarivo (2006–2007). Computing resources at the Pawsey Supercomputing Centre (WA) were used to perform BLAST searches. We would like to thank Alison Devault at MYcroarry for assistance designing enrichment baits. We give special thanks to the Morombe Archaeological Project (MAP) team and to the people of Andavadoaka, Madagascar for helping collect eggshell. The authors acknowledge the facilities, and the scientific and technical assistance of the National Imaging Facility at the Centre for Microscopy, Characterisation and Analysis, The University of Western Australia—a facility funded by the University, State and Commonwealth Governments. M.M. and M.C. are supported by Danish National Research Foundation Award PROTEIOS (DNRF128). We thank Prof. Jesper Velgaard Olsen at the Novo Nordisk Center for Protein Research for providing access and resources, which were also funded in part by a donation from the Novo Nordisk Foundation (Grant No. NNF14CC0001). We would also like to acknowledge the passing of Professor Marilyn Fogel in 2022, and thank her for her contributions to stable isotope research., Funder: Australian Research Council (DE120100107 and FT0991741 National Geography Society Easterbrook Distinguished Scientist Award Ministry of University and Research (Young researchers “Rita Levi Montalcini”) National Science Foundation Graduate Research Fellowship Program P.E.O. Scholar Award Yale Institute of Biospheric Studies Yale MacMillan Center for International and Area Studies Yale Council on Archaeological Studies Danish National Research Foundation Award PROTEIOS (DNRF128) Novo Nordisk Foundation (Grant No. NNF14CC0001), The systematics of Madagascar's extinct elephant birds remains controversial due to large gaps in the fossil record and poor biomolecular preservation of skeletal specimens. Here, a molecular analysis of 1000-year-old fossil eggshells provides the first description of elephant bird phylogeography and offers insight into the ecology and evolution of these flightless giants. Mitochondrial genomes from across Madagascar reveal genetic variation that is correlated with eggshell morphology, stable isotope composition, and geographic distribution. The elephant bird crown is dated to ca. 30 Mya, when Madagascar is estimated to have become less arid as it moved northward. High levels of between-clade genetic variation support reclassifying Mullerornis into a separate family. Low levels of within-clade genetic variation suggest there were only two elephant bird genera existing in southern Madagascar during the Holocene. However, we find an eggshell collection from Madagascar's far north that represents a unique lineage of Aepyornis. Furthermore, divergence within Aepyornis coincides with the aridification of Madagascar during the early Pleistocene ca. 1.5 Ma, and is consistent with the fragmentation of populations in the highlands driving diversification and the evolution of extreme gigantism over shorts timescales. We advocate for a revision of their taxonomy that integrates palaeogenomic and palaeoecological perspectives.