We report the evaluation results of mechanical characterization of Synechocystis sp. PCC 6803. We have constructed the force measurement system using the microfluidic chip on the microscope with optical tweezers. Indentation and force sensor probes are integrated into the microfluidic chip. Using the constructed system, we evaluated the Young's modulus of two cell groups of wild type and mutant type, which was knocked out mechanosensitive channels. They are placed in two different mediums; normal and high-osmolality condition. While there was no significant difference of stiffness between two groups in normal medium, the average value and the standard deviation of Young's modulus were different in high-osmolality condition. These results indicate the basic function of mechanosensitive channels, because there was clear relationship between the stiffness and the osmotic stress. We confirmed that the measurement system will contribute to clarify unknown function of ion channels of cyanobacteria based on relationship between environmental stress and mechanical characteristics on single cell level.