The large fluctuation in reproductive output at plant population level, called masting, has been identified in a wide range of species. The role of resource availability as one of the proximate factors for masting has attracted much attention with strong theoretical support from the resource budget model. Recently, the molecular genetic underpinning of flowering timing has been uncovered in model plant systems. Here we applied expression analysis of flowering genes to Siebold’s beech, a typical masting species in cool-temperate forests in Japan, to study the effect of resource availability on floral initiation. Four-year monitoring of flowering gene expression in naturally grown trees revealed a clear cycle of on and off years, which wwas correlated with high and low nitrogen concentration in the current year shoots, although carbohydrate availability did now show any clear relationship. Nitrogen fertilization using grafted trees resulted in a significantly higher expression in the flowering genes than controls, and all the fertilized trees flowered but no flowers were produced in the control trees. Our findings identified nitrogen as a key regulator of masting, and provide a new empirical evidence that supports the theoretically proposed mechanism of masting.