In this paper, a method is presented to identify the physical and modal parameters of multistory shear building based on substructural technique using block pulse generalized operational matrix and genetic algorithm. The substructure approach divides a complete structure into several substructures in order to significantly reduce the number of unknown parameters for each substructure so that identification processes can be independently conducted on each substructure. Block pulse functions are set of orthogonal functions that have been used in recent years as useful tools in signal characterization. Assuming that the input-outputs data of the system are known, their original BP coefficients can be calculated using numerical method. By using generalized BP operational matrices, substructural dynamic vibration equations can be converted into algebraic equations and based on BP coefficient for each story can be estimated. A cost function can be defined for each story based on original and estimated BP coefficients and physical parameters such as mass, stiffness and damping can be obtained by minimizing cost functions with genetic algorithm. Then, the modal parameters can be computed based on physical parameters. This method does not require that all floors are equipped with sensor simultaneously. To prove the validity, numerical simulation of a shear building excited by two different normally distributed random signals is presented. To evaluate the noise effect, measurement random white noise is added to the noise-free structural responses. The results reveal the proposed method can be beneficial in structural identification with less computational expenses and high accuracy.