The efficiency of the conventional, explicit finite difference time domain (FDTD) method is constrained by the upper limit on the temporal discretization imposed by the Courant-Friedrich-Lewy (CFL) stability condition. Therefore, there is a growing interest in overcoming this limitation by employing implicit, unconditionally stable FDTD methods for which time-step and space-step can be independently chosen. Unconditionally stable Crank Nicolson method has not been widely used in time domain electromagnetics despite its high accuracy and low anisotropy. This work presents a novel three-dimensional frequency dependent fully implicit Crank Nicolson FDTD method. A modified frequency dependent alternating direction implicit FDTD (FD-ADI-FDTD) method, having better accuracy than the normal FD-ADI-FDTD method, is also presented.