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In this paper, modeling and control of manipulator handling a flexible payload is considered under the parameter uncertainty and the unknown disturbance. A new sliding mode controller is proposed for manipulator handling a flexible payload based on a distributed-parameter dynamic model and hence is free from the so-called spillover instability, then extended to an adaptive scheme to cope with the upper bounds of the uncertainties were unknown. The controllers are designed to realize system trajectory tracking performance and suppress the elastic vibration. The sliding surface is designed as coupling the joint angle and angular velocity of link, as well as root strain and shear force of flexible payload. Stability of the system is proved by using Lyapunov theory. Numerical simulations result provided to verify the effectiveness of the approach presented.