In Kyoto City, there are many garden ponds which have water supplied by canal from Lake Biwa. Various kinds of fish, including endangered species which have colonized from the lake, inhabit these garden ponds, and fish variety is rich in some of them. The purpose of this study is to clarify the environmental variables affecting the species richness of fish in the limited space of garden ponds which have the same water source. Analyses using TWINSPAN and CCA have revealed that the diversity of micro-habitat has a very important role in species richness which depends on the establishment of symbiotic relations in garden ponds. Existence of a stream and/or a high turnover rate of water were found to contribute to the diversity of micro-habitats in garden ponds. These results could contribute to the planning and design of ponds as wildlife habitats.