This paper presents a discrete-time design of a dual-stage actuator control system with sliding mode for computer disk drives. A state estimator based discrete-time boundary layer sliding mode control scheme is developed for a dual-stage actuator, which consists of a voice coil motor and a microactuator. Considering dominant microactuator flexible mode dynamics and the interaction between the two actuators, an optimal sliding hyperplane is designed to maximize their cooperation so as to attain desired responses. An application example demonstrates the utility of the proposed sliding mode dual-stage actuator control scheme for track-seek in the microactuator range, settle, and track-follow.