Reproductive phenology was observed over three years in a Eucalyptus grandis seed orchard in Madagascar to determine the impact of geographic differences of parental selections on the expected genetic composition of seed crops. Pollen flow (observed pollen cloud) was deduced from a paternity assignment based on sampling from one year's seed production. The two approaches were used to verify whether knowledge of phenology is sufficient to predict the genetic quality of the seeds collected. Despite the high flowering level, with a constant cycle over three years, the results demonstrated wide reproductive phenological differences associated with the parents' origin, suggesting putative pollination disequilibrium. From both observed and expected pollen clouds, the results showed preferential mating among different provenances, which has consequences for seed crop composition. Phenological observations, which can be made inexpensively, can be used to promote methods of effective seed orchard management in order to improve the genetic quality of seeds.