Durian (Durio zibethinus) has emerged as an economically and agriculturally important crop as it is one of the most popular seasonal fruits grown in Thailand. It is heavily consumed within the local market as well as exported to other countries. During a survey of the durian plantation areas in Chanthaburi Province in eastern Thailand in 2022, dieback disease symptoms were observed in a high number of durian trees in the area. The observed field symptoms included leaf defoliation and branch dieback. The aim of this research was to investigate and confirm the causal agent to prevent any future outbreaks. Initial observations of the symptoms and morphological studies concluded the pathogen belongs to Nectriaceae. For further identification, the potential causal organisms were isolated from the infected stems and branches through the tissue isolation method. Extensive morphological studies combined with multilocus phylogenetic analyses of eight isolates were used for accurate identification of the pathogen. The eight isolates placed in Microcera and Neocosmospora clades with similar morphological characters of these two genera. The results from our study will be important for accurate identification and prevention of this disease in durian cultivations in the future.