The results of phytosociological research conducted on the fern vegetation of rock crevices and clefts of the Pamir-Alai Mountains in Tajikistan are presented. During field surveys done in 2010–2013, 78 phytosociological relevés were sampled. Plant species were recorded according to the Braun-Blanquet cover-abundance scale. A synopsis of the fern communities of the montane and high altitude zones in Tajikistan is proposed. In the examined vegetation plots, species of 9 ferns, 58 angiosperms and 13 mosses were recorded. The most frequent ferns were: Cystopteris fragilis, Cheilanthes persica, Asplenium ruta-muraria, Asplenium ceterach, Adiantum capillus-veneris and Cryptogramma stelleri. Six plant associations could be distinguished: Cheilanthetum persicae, Cryptogrammetum stelleri, Soncho transcaspici-Adiantetum capilli-veneris, Asplenio-Ceterachetum officinarum, Asplenio-Cystopteridetum fragilis, and Asplenietum trichomano-rutae-murariae. The first three associations are described for the first time. The main factors determining the species composition of classified associations are elevation range, microhabitat humidity and moss cover. A minor role is played by the geographic distribution range and rock type.