Seismic isolation and energy dissipation systems are innovative strategies for seismic design, and upgrade or retrofit of bridges. In a retrofit design, base isolation devices can be easily incorporated into existing bridges to replace conventional bearings and to improve the overall structural performance. In this paper, an optimal cost base isolation design or retrofit design method of bridges subject to transient earthquake loads is studied. The aim of this study is to push forward the concept of retrofit design optimization of structures using the special case of isolation retrofit design. This can be achieved by combining nonlinear time history analyses with optimization procedures to select base isolators to achieve the objective of minimum cost of the isolation system while satisfying certain design requirements. Such design procedures are iterative and involve repeated analyses before an optimum solution can be achieved. Due to the discrete nature of the problem, an improved genetic algorithm (GA) – Micro-GA is employed to find the optimal solutions. An example of the optimal design of a highway bridge is presented and the minimum cost expense of isolation system is achieved with improved structural response under transient earthquake loads.