Historic records indicate that in 1909 the remains of 17 Maronite patriarchs were exhumed from their primary burial location and transferred to a collective secondary burial inside the Saint Marina chapel in an underground cave at the Qanubin monastery in the Northern Lebanese mountains. We used Church records, iconography, archaeology, anthropology, and ancient DNA (aDNA) analyses to investigate whether the remains found in the chapel might belong to the patriarchs. Further, we hoped to identify the remains of patriarch Estephan El Douaihy, one of the 17 patriarchs who was among those said to be buried in the chapel and who is in the process of being canonized by the Vatican. The entire secondary burial was excavated by horizontal ‘décapage’. Pairing of bones, and reconstruction were undertaken, and the Minimum Number of Individuals (MNI) was identified. Age at death was determined through senescence indicators and sex determination was determined from pelvic bone observations. There were only 16 complete crania represented in the collection, and these were targeted for aDNA analyses. The complete mitochondrial genomes were sequenced for all 16 samples and Y-chromosome haplogroups were able to be determined for four individuals. The evidence from the funerary stele, historical church records, osteological analyses and aDNA analyses when combined provide strong evidence to suggest that the 16 complete skulls present in the burial likely belong to 16 of the patriarchs exhumed in 1909.