Taiwan is famous for the growth of varieties of Ganoderma. However, there is a lack of a systematic taxonomic method for analyzing these fungi. In this study, we have proposed a taxonomic system by incorporating a model of bicriteria fuzzy cluster analysis. After performing the cluster analysis with the proposed method on the 2899 given specimens, we suggest 12 well-defined species of which 8 are fully consistent with the current taxonomy. Thus, based on current taxonomy the unmatching rate is 33%, which includes the data error rate of 29.1% and the model error rate of 3.9%.