The Aldabra giant tortoise is the only surviving lineage of the Malagasy megafauna, which went extinct due to human activities over the last millennium. In 2018, the first rewilding project was launched at the Anjajavy Reserve (NW Madagascar), using 12 founders of unknown origin. They started to mate in 2019, but genetic proximity between individuals and their reproductive output remains to be determined for optimal management of the newly established population. Here, we used 29 microsatellite loci to analyze the genetic diversity of native populations from Aldabra, a coral atoll 420¿km from Madagascar, to assign Anjajavy founders to specific genetic groups and assess how well they represent the overall genetic diversity in the native range. Additionally, five of these loci allowed us to investigate the diversity of the genomic region containing the Major Histocompatibility Complex (MHC) genes. The non-MHC microsatellite data were also used to investigate the past demography of the species using a stepwise mutation model (VarEff). Finally, we evaluated the contribution of Anjajavy founders to the offspring. First, the clustering analysis identified two main genetic groups in Aldabra, and demographic inferences then support that population size fluctuations were strongly shaped by climatic shifts and sea-level changes on the atoll. Both genetic groups are represented among the Anjajavy founders, who most likely originated from the southern island of Aldabra. However, the founders contributed unequally to the offspring, as most juveniles analyzed were the result of mating between individuals from the two groups, leading to a significant global increase in heterozygosity in the offspring. We propose measures to minimize inbreeding and maintain genetic diversity within the Anjajavy population, thereby enhancing its potential for long-term viability.