A field survey was undertaken on various ornamental and native trees in Kish Island (Hormozgan province) to determine the fungal trunk pathogens associated with branch and trunk diseases. Between April 2016 and January 2017, wood samples were collected from various trees showing yellowing, defoliation, canker, sooty canker, die-back and decline symptoms. Small pieces (3-5 mm) of discolored wood tissues from the lesion margins were sterilised by sodium hypochlorite, rinsed in sterile water and then were placed onto potato dextrose agar (PDA) or malt extract agar (MEA) amended with tetracycline hydrochloride in petri dishes. Petri dishes were incubated at 25°C in the dark for 8-16 days and all colonies were transferred to fresh media. All isolates were purified, using hyphal tip technique. Representative isolates were identified based on morphology as well as molecular and phylogenetic analysis of the internal transcribed spacer region (ITS1-5.8S-ITS2) and a partial sequence of the translation elongation factor 1α (EF-1α) genes using the primer pairs ITS1/ITS4 and EF1-728F /EF1-986R, respectively. During this survey, 81 fungal isolates morphologically resembling species within Botryosphaeriaceae family (fast growth and greenish-grey to dark colonies) were obtained from Prosopis cineraria and Albizia julibrissin trees. Based on morphological and molecular characteristics these isolates were identified as Lasiodiplodia theobromae (61 isolates: 49 isolates from P. cineraria and 12 from A. julibrissin) and Neoscytalidium hyalinum (20 isolates: 10 isolates from P. cineraria and 10 isolates from A. julibrissin). This study provides the first record of L. theobromaea and N. hyalinum from P. cineraria and A. julibrissin in the world.