A review of recent literature and the research effort underlying this dissertation indicates that fractional order differential equations have significant potential to advance dynamical system methods broadly. Particular promise exists in the area of control and estimation, even for systems where fractional order models do not arise “naturally”. This dissertation is aimed at further building of the base methodology with a focus on robust feedback control and state estimation. By setting the mathematical foundation with the fractional derivative Caputo definition, we can expand the concept of the fractional order calculus in a way that enables us to build corresponding controllers and estimators in the state-space form. For the robust eigenstructure assignment, we first examine the conditioning problem of the closed-loop eigenvalues and stability robustnesss criteria for the fractional order system, and we find a unique application of an n-dimensional rotation algorithm developed by Mortari, to solve the robust eigenstructure assignment problem in a novel way. In contradistinction to the existing Fractional Kalman filter developed by using Gru ̈ndwald-Letnikov definition, the new Fractional Kalman filter that we establish by utilizing Caputo definition and our algorithms provide us with powerful means for solving practical state estimation problems for fractional order systems.