Genotypic data at twelve loci for the analysis of the spatial genetic structure of 766 seedlings from 6 different seedling cohorts of Abies alba Mill., the European silver fir, at its range margin, in Mont Ventoux, France. Seedlings were sampled in an intensive study plot of 0.79 ha on Mont Ventoux (latitude: 44°10’56” N - longitude: 5°17’01” E - elevation: 1400-1450 m above sea level) at the southwestern-most tip of the Alps in France All seedling are geolocalized and their height are attributed to the following cohorts: C1 (20-50 cm in height): 152 individuals; C2 (50-100cm in height):183 individuals; C3 (100-200 cm in height): 156 individuals; C4 (200-300 cm in ): 78 individuals; C5 (300-500 cm in height): 109 individuals; C6 (>500 cm in height): 88 individuals. The genetic data include ten biallelic bi-parentally inherited isozyme loci and two paternally-inherited chloroplast microsatellite (cpSSR) loci. Isozyme data are coded as genotypes with two alleles at each locus (e.g. an individual scored "12" indicates that the electrophoretically detected genotype was heterozygote for alleles "1" and "2"). cpSSRs data are coded as length variants (e.g. an individual scored "136" indicates that the electrophoretically detected variant size was 136 base pairs long Measurements and genetic scoring were done in 1998. The data are sufficiently resolved to address issues related to spatial genetic structure in a relatively inbred population. They can also be used for meta-analyses and for teaching purposes.