The present invention analyzes a microbial flora with high accuracy that is included in an activated sludge on which water treatment is performed. The computer 10 of a microbial flora analysis system 1 is provided with an input unit 12 for inputting a plurality of data groups that include information indicating the base sequence of a gene of each of a plurality of microbes present in an activated sludge on which water treatment is performed, a similarity calculation unit 13 for calculating similarity between the data groups on the basis of the base sequences included in the inputted data groups, and a coordinate calculation unit 14 for calculating the coordinates on a multi-dimensional space of each of the data groups on the basis of the calculated similarity.
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