Control algorithms are the most important aspects in successful control of structures against earthquakes. In recent years, intelligent control methods rather than classical control methods have been more considered by researchers, due to some specific capabilities such as handling nonlinear and complex systems, adaptability, and robustness to errors and uncertainties. However, due to lack of learning ability of fuzzy controller, it is used in combination with a genetic algorithm, which in turn suffers from some problems like premature convergence around an incorrect target. Therefore in this research, the introduction and design of the Fuzzy Cooperative Coevolution (Fuzzy CoCo) controller and Adaptive Neural-Fuzzy Inference System (ANFIS) have been innovatively presented for semi-active seismic control. In this research, in order to improve the seismic behavior of structures, a semi-active control of building using Magneto Rheological (MR) damper is proposed to determine input voltage of Magneto Rheological (MR) dampers using ANFIS and Fuzzy CoCo. Genetic Algorithm (GA) is used to optimize the performance of controllers. In this paper, the design of controllers is based on the reduction of the Park-Ang damage index. In order to assess the effectiveness of the designed control system, its function is numerically studied on a 9-story benchmark building, and is compared to those of a Wavelet Neural Network (WNN), fuzzy logic controller optimized by genetic algorithm (GAFLC), Linear Quadratic Gaussian (LQG) and Clipped Optimal Control (COC) systems in terms of seismic performance. The results showed desirable performance of the ANFIS and Fuzzy CoCo controllers in considerably reducing the structure responses under different earthquakes; for instance ANFIS and Fuzzy CoCo controllers showed respectively 38 and 46% reductions in peak inter-story drift ($J_1$) compared to the LQG controller; 30 and 39% reductions in $J_1$ compared to the COC controller and 3 and 16% reductions in $J_1$ compared to the GAFLC controller. When compared to other controllers, one can conclude that Fuzzy CoCo controller performs better.