We introduce new computer algorithm of multiple alignment as an application of "Simulated Annealing" method. Simulated Annealing has been applied to some combinational optimization problems such as travelling salesman problem. After giving short mathematical explanation of this method, we construct genetic distance and matrix corresponding to the object function in the annealing theory for the multiple alignment. Our method is better than other alignment in the sense that we obtain a result having a smaller value for the genetic distance. We discuss further development along on new method.