This paper proposes a self-assembly fabrication method of microwells and investigates the effect of surface treatment for the cell trapping. The target cell is unicellular cyanobacterium Synechocystis sp. strain PCC 6803, which has been widely investigated as a model organism for photosynthesis. The self-assembly monolayer of polystyrene particles (3.0 mu m diameter) etched by reactive-ion etching was used as a template of polydimethylsiloxane molds. The well diameter in the mold could be controlled by the etching time. The cell-trapping efficiency was discussed with the viewpoint of hydrophilically treatment and poly-L-lysine treatment on the well arrays.