CE-SSCP based genetic analysis method can discriminate differences in conformation of single-strand DNA molecules derived from their sequences. Microchip-based CE-SSCP (μCE-SSCP) is one of promising genetic analysis system due to the less sample consumption, fast analysis, and cost-effectiveness as well as convenience in use. However, the most critical limitation of μCE-SSCP is low separation resolution. In our previous research, PEO-PPO-PEO triblock copolymer matrix was demonstrated that significantly increase the separation resolution on benchtop CE-SSCP. Due to dynamic coating and high-density sieve forming ability of PEO-PPO-PEO triblock copolymer matrix, the limitation of μCE-SSCP could be overcome by utilizing the triblock copolymer matrix.