SINS attitude matrix can not be calculated directly from the output of gyro and accelerometer due to the interference of strong angular motion and linear vibration.In order to solve the problems,a novel HMM/KF(hidden Markov model/Kalman filter) based Wahba initial aligement aligorithm was proposed,the interference caused by angular motion and linear vibration were prefiltered through HMM/KF.Compared with conventional digital filters using a priori fixed cutoff frequency ,this method has a stronge adaptive characteristic.Mooring alignment experiment results show that the presented method can accomplish alignment quickly even in the presence of angular motion and linear vibration interference without the coarse alignment process.