The present invention provides for a method for selecting an antimicrobial agent, which comprises a microbe analyzing step in which microbes in the microbial biota of a sample are analyzed based on base sequence of DNA and an antimicrobial agent selecting step comprising performing search in a data base storing data for industrial antimicrobial agents applicable to the analyzed microbes recited at effective concentrations, picking up industrial antimicrobial agents effective for the microbial biota, dominant microbe or specific microbe(s) in the sample analyzed in the above microbe analyzing step and selecting among the picked up ones an industrial antimicrobial agent, which method permits to select an antimicrobial agent that is optimum for the treatment in a simple and assured manner within a brief time and to grasp whether the effect of the antimicrobial agent is revealed or not in a simple and assured manner within a brief time, by utilizing this selecting method for the selection of antimicrobial agent, for example, in an antimicrobial treating, in monitoring of the antimicrobial effect, in slime control in paper manufacturing process courses and in microbe inhibition in paper manufacturing process courses, whereby troubles caused by growth of microbes can be prevented beforehand.