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Many studies have focused in designing a set of good DNA sequences as it is one of the crucial tools in improving the reliability and efficiency of DNA computing. In this paper, an improved model of Ant Colony System is developed in optimizing DNA sequences design. The proposed model suggests that each artificial ant represents a possible solution of the DNA sequences design problem. This differs from the previous Ant Colony System approached where a number of artificial ants are required to represent a possible solution. In the implementation, four objective measures and two constraint measures are employed to obtain a good set of DNA sequences. The performance of the proposed model is evaluated by comparing the result with existing Ant Colony System model and other published sequence design method. The experimental result shows that the proposed Ant Colony System model outperformed the existing Ant Colony System model.