Rough bark disease (RBD) damages the peel of cinnamon (Cinnamommum zeylanicum), the economically important part of the plant. A total of 405 plant samples representing four distinct symptom development stages of RBD were collected from five cinnamon‐growing districts of Sri Lanka. Epiphytic and endophytic fungi dwelling on different tissues of the stems were isolated using another set of healthy and RBD‐infected plants. Different tissues of healthy and RBD‐infected stems representing the symptom development stages and districts of cinnamon cultivation resulted in a total of 2432 fungal isolates. Fungal profiles associated with different stem tissues in healthy and RBD‐infected plants during the pathogenesis were determined by colony and spore morphology of isolated fungal isolates and DNA sequencing of PCR products by ITS1 and ITS4 primers. Pathogenicity was tested using consistently associated 138 isolates on detached stem pieces. Subsequently, field‐grown plants were inoculated with three highly virulent isolates among the 138 isolates. Pestalotiopsis, Colletotrichum, Botryodiplodia, and Phomopsis were the core fungal genera in the four symptom development stages with a varying abundance. The four genera were infectious having different degrees of virulence in terms of lesion development on stems. Composition and relative abundance of fungal profiles were compared in different stem tissues of healthy and RBD‐infected plants at distinct symptom development stages. Results revealed the presence of a core fungal genera in both healthy and RBD‐infected plants but a fluctuation of their abundance among different tissues and symptom development stages. RBD can be deduced as a complex fungal disease than a unimicrobial infection.