Plant species often show different taxonomic and functional characteristics between limestone forests (LFs) and non-limestone forests (NLFs) in tropical regions. Pteridophyte species are one of the major components in tropical rainforests; however, the morphological and physiological characteristics of pteridophytes occurring in LFs are poorly understood. We evaluated the differences in seven leaf functional traits between pteridophyte species in LFs and NLFs in southwest China. We measured leaf water content, morphological traits including leaf size, leaf thickness, stomatal length, and stomatal density, and physiological traits including stomatal conductance and photosynthetic rate from a total of 25 species. We found that pteridophytes had thicker and smaller leaves with lower stomatal density and lower stomatal conductance in LFs compared to NLFs, probably reflecting their adaptations in water use strategies. These differences, however, became non-significant when we accounted for phylogenetic relationships, suggesting that phylogenetic conservatism shapes trait differences and ultimately species composition in LFs and NLFs. Some species that were commonly found in both LFs and NLFs demonstrated intraspecific variation between forest types, with lower stomatal density in LFs. Our findings suggest that only a handful of pteridophyte species can adapt their water use strategies in both LFs and NLFs, and thus adaptative radiation is unlikely to have occurred.