In the present central Saharan conditions, the Laperrine's olive regeneration has never been observed and its populations are locally threatened. The production of plants originating from seeds was proposed as a multiplication strategy. In order to determine the impact of sexual reproduction, seeds issued from ten mothers (sampled from four locations in the Hoggar, Algeria) were genotyped using microsatellites. Compared to the initial population, a significant lost of allelic richness was revealed, indicating that our seed sampling was not representative of the local gene diversity. Paternity analyses allowed measurement of the effective pollen-mediated gene flow within patches. Preferential mating between some genotypes was revealed. A trend for a higher multipaternity on seeds collected on trees from relatively large patches was also observed. Lastly, seedlings issued from trees of small patches displayed low growth performance. The implications of our observations in the development of an efficient conservation strategy by seeds are discussed.