The circadian system is an endogenous oscillatory rhythm that governs many aspect of biological functions in organisms. Organisms can perform at their best when this circadian rhythm is properly coordinated with their biological functions. In plants, one of the important biological functions mediated by the circadian system is flowering time. Proper flowering time especially in grain-bearing crops would ensure good productivity, which is important for the agricultural sector. One way to achieve this is to have a good control and decision support system that can properly manage the flowering time. To design such system, a model relating the circadian system and flowering time is needed. Conventional models that have been used to model circadian system for flowering time are nonlinear and they are difficult to be used for control design. In this paper, we build a model of circadian system for flowering time using system identification techniques. Models built using system identification are usually simple and useful for control design. We show that a simple linear model is able to describe the circadian system for flowering time and this model is sufficient for control design. A controller is designed using this model and the performance of the controller is shown to be good through simulation examples.