It has long been argued that related asexual and sexual taxa have different distribution patterns. In general, apomictic angiosperms are believed to occur preferentially at higher latitudes and elevations compared to their sexual relatives. It is thus expected that the frequency of apomixis increases with latitude or from warmer to colder climatic regions. However, despite the significant role played by apogamy in fern evolution and diversification, the distribution pattern of apogamous ferns and lycophytes has received little attention. To clarify the ecological diversity pattern and evolutional diversification of apogamous ferns, we analysed a variety of apogamous fern species with reference to latitude, elevation and climatic factors, and reconstructed the ancestral state and estimated the divergence time of Japanese apogamous ferns. Our results on the distribution of apogamous ferns along these two gradients suggest a decline in the proportion of apogamous ferns towards high latitudes and elevations. Temperature was correlated with the proportion of apogamous ferns along both gradients, and the seasonality of precipitation was correlated with the proportion of apogamous ferns along latitude. Reconstruction of ancestral state and estimates of divergence time showed that the crown groups of apogamous ferns diversified less than 15 Ma. The results of our ecological and phylogenetic approaches reinforce the hypothesis based on previously reported phylogenetic results in which the apogamous ferns appears to be correlated with strongly seasonal climates such as the Asia monsoon.