The elephant birds of Madagascar (Aves: Aepyornithidae) were large, flightless ratites that became extinct around a millennium ago. These birds offer excellent models to study many aspects of evolution, including speciation and extinction, as well as test biogeographic hypotheses and characterise the genetic basis of island phenotypes. In these endeavors, ancient DNA (aDNA) from elephant birds is essential. However, it has been challenging to recover aDNA from skeletal fossils due to their rarity and the warm climate of Madagascar, which is not conducive to aDNA preservation. With approximately 3% endogenous aDNA retrievable from elephant bird eggshell, it is a promising substrate for recovering high-quality aDNA. Using aDNA extracted from fossil eggshell, coupled with target enrichment and next-generation sequencing techniques, we recover complete mitochondrial genomes as well as nuclear loci, and use these to investigate the placement of elephant birds within the avian phylogeny, date their divergence from other birds, revisit elephant bird taxonomy, and provide the first analysis of elephant bird phylogeography. These results offer the first molecular insight into elephant bird biodiversity and speciation, and advocate for a major revision of elephant bird systematics. We foresee that elephant bird whole genome recovery is ultimately achievable, and will provide further insights into the evolution these birds.