This paper studies the adaptive fault-tolerant control problem for biological systems with the invasion of alien species. Firstly, to overcome the difficulty of dealing with nonlinear terms in the system, the T-S fuzzy method is applied to obtain the T-S fuzzy biological systems. Then, an augmented matrix is developed for the T-S fuzzy system, and a sliding mode observer is constructed to estimate the state vector, sensor faults, sensor failure and external disturbances. In addition, an observer-based adaptive sliding-mode control law is designed to ensure the stability of the closed-loop biological system. Finally, a simulation example is presented to illustrate the effectiveness of the proposed method.