Identification of the nonlinear hysteretic behavior of a reinforced concrete (RC) bridge pier subjected to earthquake loads is carried out based on acceleration measurements of the earthquake motion and bridge responses. The modified Takeda model is used to describe the hysteretic behavior of the RC pier with a small number of parameters, in which the nonlinear behavior is described in logical forms rather than analytical expressions. Hence, the modified extended Kalman filter is employed to construct the state transition matrix using a finite difference scheme. The sequential modified extended Kalman filter algorithm is proposed to identify the unknown parameters and the state vector separately in two steps, so that the size of the problem for each identification procedure may be reduced and possible numerical problems may be avoided. Mode superposition with a modal sorting technique is also proposed to reduce the size of the identification problem for the nonlinear dynamic system with multi-degrees of freedom. Example analysis is carried out for a continuous bridge with a RC pier subjected to earthquake loads in the longitudinal and transverse directions.