Abstract• Microsatellite markers were used to describe the genetic structure and variability of early, intermediate and late phenological forms of European beech (Fagus sylvatica L.). Two hundred and seventy individuals from three populations located in southern Poland were divided into three forms according to the phenological criterion -bud burst, and analyzed for allelic variation at five highly polymorphic microsatellite loci.• Population differentiation was moderate and differed significantly among phenological forms. • Analysis of Molecular Variance (AMOVA) revealed different genetic structures characteristic of respective phenological forms of beech. The amount of within-population variability increased with the delay of the beginning of vegetation and amounted to 64%, 77% and 90% of total variability, depending on phenological form. A similar trend was found in average pairwise genetic distance between individuals belonging to a given phenological form (11.78, 11.85 and 12.22, from early to late forms).• Our results demonstrate the importance of late spring frosts as a factor influencing the genetic structure of beech, and as a cause of the decrease in genetic variability as well as the increase in population differentiation proportional to the degree of phenological earliness.