During the Spanish Civil War (1936–1939) and the subsequent dictatorship, approximately 114,000 people are estimated to have disappeared, and more than 80 years later only a small fraction has been identified. The cemeteries of Orduña and Amorebieta-Etxano represent two of the most significant exhumed mass graves in the Basque Country, where autosomal STRs, YSTRs and/or mitochondrial DNA markers were analyzed from skeletal remains for comparison with profiles from reference relatives. However, the number of identifications differs notably between the two sites. In Orduña, between 1937 and 1941 there was concentration camp for prisoners of war that later became a central prison. Official documentation lists the individuals who died there due to extreme conditions of insalubrity and hunger, greatly facilitating the location of relatives, mostly from southern Spain, and improving the likelihood of genetic matches. In contrast, in the case of Amorebieta-Etxano, which is the largest exhumed mass grave in the region, individuals buried there likely died in nearby combat or in the military hospital. Although death records exist in many cases, burial locations were not documented, making the search for reference relatives considerably more difficult and resulting in fewer identifications. Occasionally, identification tags from the Army of Euskadi were recovered, offering clues but not definitive evidence. This comparison underscores the critical role of historical documentation as a complementary and valuable tool in genetic analysis for the identification of Civil War victims. Despite the complexities, efforts to locate new reference relatives remain ongoing to maximize the number of identifications achievable.