The ancient animal catacombs throughout the Egyptian deserts harbour millions of well-preserved mummified Sacred Ibises (Threskiornis aethiopicus), the source of which remains unknown. It is thought that since 600 BC, pilgrims presented the mummified Ibises as ‘votive’ offerings to Thoth, the Egyptian God of wisdom. We have recently estimated the radiocarbon ages of mummies provenience from Saqqara, Roda and Thebes in Egypt age between 2220–2430 yr. BP . The demand for Sacred Ibis was so great it was estimated that each year ~10,000 mummies were interred at one catacomb alone. Such massive numbers suggest that ancient Egyptians kept and reared Ibis on an industrial-scale. However, there is limited evidence in ancient writings that support this suggestion. Sacred Ibis were once prevalent in Egypt but were driven to extinction as early as the mid 1800's. To investigate the likely farming methods employed by these ancient people, we used ancient DNA technology and targeted hybridization enrichment methods to retrieve complete mitochondrial genomes from ancient Sacred Ibis mummies, together with the genomes of contemporary individuals from widespread African populations. Unexpectedly, we show a remarkably high level of mitochondrial genetic variation among ancient Egyptian Sacred Ibis, very similar to that found for all modern wild African populations. Mitochondrial haplotype phylogenies and network analyses showed no genetic evidence to support the existence of a single large centralised Sacred Ibis farm in Ancient Egypt, nor for the presence of smaller localised farms. However, our results support the hypothesis that the ancient Egyptians likely complemented captive Sacred Ibis stocks held in localised enclosures, via multiple wild sources. This method would have helped maintain the health of these populations and facilitated the high Ibis mummies supply in response to the year-by-year demand for sacrificial birds.