The paper deals with the application of the extended Kalman filters in the control structure of a two-mass drive system. In the first step only linear extended Kalman filter was used for the estimation of mechanical state variables of the drive including load torque value. The estimation algorithm showed good robustness to mechanical parameters variations. For the system with some parameters changing in the wide range, simultaneous estimation of the state variables and chosen system parameters is required. For this reason the non-linear extended Kalman filter, which estimates simultaneously state variables and mechanical parameters of the two-mass drive system, was developed. Parameters of covariance matrices of used Kalman filters were set using the genetic algorithm. Both proposed estimators were investigated in simulation and experimental tests, in the open-loop operation and in the state-feedback control system of the two-mass system.