This work is devoted to application of Fractional Derivative in the identification of nonlinear system as well as creation of a control system for nonlinear dynamical system of fractional order. In the first part of the work reader is referred to the theoretical foundations of fractional derivative and its applications to the theory of systems, identification and system control. In subsequent parts will be considered FOMCON ("Fractional-order Modeling and Control")—a tool for the identification of fractional order systems and the creation of fractional control systems, and its application. There will also be proposed methods for improving the work of FOMCON and their practical application for identification. Finally, the control system will be established for the nonlinear object represented by a system of two coupled tanks and also an experimental system. All used in this paper calculations, simulations, and algorithms are made in an environment MATLAB / FOMCON.