In Japan, rice paddies play an important role as a substitute habitat for wetland species, and support rich indigenous ecosystems. However, since the 1950s, agricultural modernization has altered the rice paddy environment, and many previously common species are now endangered. It is urgently necessary to evaluate rice paddies as habitats for conservation. Among the species living in rice paddies, frogs are representative and are good indicator species, so we focused on frog species and analyzed the influence of environmental factors on their habitat use. We found four frog species and one subspecies (Hyla japonica, Pelophylax nigromaculatus, Glandirana rugosa, Lithobates catesbeianus, and Pelophylax porosa brevipoda) at our study sites in Shiga prefecture. For all but L. catesbeianus, we analyzed the influence of environmental factors related to rice paddy structure, water management and availability, agrochemical use, connectivity, and land use on breeding and non-breeding habitat use. We constructed generalized additive mixed models with survey date as the smooth term and applied Akaike's information criterion to choose the bestranked model. Because life histories and biological characteristics vary among species, the factors affecting habitat use by frogs are also expected to differ by species. We found that both breeding and non-breeding habitat uses of each studied species were influenced by different combinations of environmental factors and that in most cases, habitat use showed seasonality. For frog conservation in rice paddies, we need to choose favorable rice paddy in relation to surrounding land use and apply suitable management for target species.