This paper presents an adaptive control allocation technique for over-actuated systems. The online actuator selection algorithm is used to select the best group of actuators. Also, a multi-objective cost function is utilized for the allocation unit. The virtual and actual control signals in the control allocation methodologies are linked by the effectiveness matrix. In many practical systems, the elements of the effectiveness matrix may vary due to changing operating conditions, nonlinearities, ageing, disturbances and faults. Hence, an online algorithm for estimation of the entries of the effectiveness matrix is presented in this paper. Estimation of the effectiveness matrix will be used for the proposed adaptive actuator selection strategy, employing the Actuator Effectiveness Index (AEI). The AEI is calculated for all the actuators, and the best group of actuators will be subsequently selected. Finally, simulation results are used to show the effectiveness of the proposed methodology.