This study aimed to demonstrate that stone walls are habitats for rare ferns and lycophytes in Japan. A survey on 47 Red Data Books (RDBs) published in each prefecture in Japan, revealed the descriptions of 47 fern and lycophyte species (equivalent to 6.5% of all native species of ferns and lycophytes in Japan) designated as near threatened or above in the RDBs and growing on stone walls in Japan. Eleven of these species were listed in the prefectural RDBs as well as in the national RDB of Japan. Overall, 40 species (85.1%) had a preferred original habitat of cliffs or rocky outcrops, and 24 species (51.1%) preferred the forest floor. The high number of identified species that prefer cliffs or rocky outcrops supports the Urban Cliff Hypothesis, which states that man-made structures such as urban buildings and walls serve as alternatives to cliffs, rocky outcrops, or screes as alternative habitat. However, in previous domestic studies that documented fern and lycophyte species growing in established hardscapes in Japan, the most frequently occurring species were mostly weedy or ruderal. As there are few studies on the composition of species growing on stone walls in Japan, more studies must investigate this aspect as well as examining the variation in species composition because of the differences in species pools, climatic conditions, or geological background.