Pteridophyta is valuable as an environmental indicator within the city matrix. In this study, the relationships between the species composition of pteridophytes and environmental factors (especially micro-landform types) was investigated using DCA, TWINSPAN and ANOVA in fragmented forest patches within the city matrix of Kyoto. In consequence, differences of pteridophytes species composition corresponded to differences of micro-landform types. Lower side slopes and bottom lands were suitable for many species (e.g., Polystichum polyblepharum, Dennstaedtia scabra). Upper side slopes and crest slopes were also suitable for some species (e.g., Dryopteris championi, Dicranopteris linearis, Gleichenia japonica). Therefore, sets of these micro-landform types should be conserved for preservation of pteridophytes species diversity.