Drynaria quercifolia is an epiphytic fern often exposed to water- and light-stressed environments. One distinct ecophysiological adaptation of epiphytic ferns is their symbiotic relationship with fungi. This is the first study undertaken to explore the phylogenetic relationship, colonization, occurrence rate, and diversity of RSF found in D. quercifolia. Two hundred seventy-eight RSF isolates were collected from 300 representative root segments. Genomic DNA of the RSF was extracted, and the ITS (internal transcribed spacer) region of the 18S ribosomal DNA (rDNA) was sequenced. Thirteen species were recorded. Eight of the 13 RSF were identified up to the species level using the Basic Local Alignment Search Tool nucleotide search program (BLASTn) to their closest type match available on the databank of NCBI. However, five RSF were undescribed. The phylogenetic relationship of RSF was determined using Molecular Evolutionary Genetics Analysis (MEGA6), and four distinct monophyletic groups were formed: Sordariomycetes, Eurotiomycetes, Saccharomycetes, and Mucoromycotina. The computed colonization rate (92.67%) implies the abundance of RSF in the roots of D. quercifolia where several species of the genus Trichoderma were found to occur very frequently. Sites 2 and 5 possess the highest temperature, the highest light intensity, and the lowest substrate moisture content common in a stressful epiphytic habitat. Despite these conditions, the two sites manifested the highest RSF isolate diversity among the five tree-collection sites. Understanding the diversity and the presence of dominating RSF is necessary to determine their principal impact on ecosystem functioning. These principal factors explain their effects on increased plant productivity, nutrient acquisition, and environmental adaptation.