Objectives We describe a method to identify human remains excavated from unmarked graves in historical Quebec cemeteries by combining parental-lineage genetic markers with the whole-population genealogy of Quebec contained in the BALSAC database. Materials and methods The remains of six men were exhumed from four historical cemeteries in the province of Quebec, Canada. DNA was extracted from the remains and genotyped to reveal their mitochondrial and Y-chromosome haplotypes, which were compared to a collection of haplotypes of genealogically-anchored modern volunteers. Maternal and paternal genealogies were searched in the BALSAC genealogical record for parental couples matching the mitochondrial and the Y-chromosome haplotypic signatures, to identify candidate sons from whom the remains could have originated. Results Analysis of the matching genealogies identified the parents of one man inhumed in the cemetery of the investigated parish during its operating time. The candidate individual died in 1833 at the age of 58, a plausible age at death in light of osteological analysis of the remains. Discussion This study demonstrates the promising potential of coupling genetic information from living individuals to genealogical data in BALSAC to identify historical human remains. If genetic coverage is increased, the genealogical information in BALSAC could enable the identification of 87% of the men (n = 178,435) married in Quebec before 1850, with high discriminatory power in most cases since >75% of the parental couples have unique biparental signatures in most regions. Genotyping and identifying Quebec's historical human remains are a key to reconstructing the genomes of the founders of Quebec and reinhuming archeological remains with a marked grave.