In this paper, we experimentally revealed that the microscale surface topography of anodes strongly affected the performance of Microbial Fuel Cells (MFC). One of the problems MFC involves is its low power. The generated power by MFC is considered to be strongly affected by the interaction between organic bacteria and inorganic electrode surface. We consider that given the bacteria size of several micrometers may play crucial roles. We prepared seven types of anode electrode which had different microscale surface topography, and experimentally found that MFC performance depended on the contact areas between the bacteria and anode and MFC exerted its maximum power with the anode containing micro holes 5~7 μm in diameter when the contact areas were largest.