Morphological characteristics of authentic cultures of Pestalotiopsis isolates  using scanning electron microscop (SEM) revealed that, no presence of pycnidia for  all examined Pestalotiopsis isolates, that produced acervuli only . Acervuli    size ranged between 350 – 800 μ in length to 270 – 500 μ in width.  Isolates varied in its ability to utilize different carbon sources. There were significant differences in the growth of Pestalotiopsisisolates in different carbon sources containing medium. Maltose gave maximum mean dry weight of mycelial growth. Ammonium nitrate recorded the maximum growth of Pestalotiopsis isolates as the nitrogen source, followed by  potassium nitrate. On the other hand, the minimum mycelia dry weight of the fungus was in Aspartic acid containing media. Sporulation was dense where sodium nitrate was used as the nitrogen source, and deprived when asparagine was used.  The genetic variation between fifteen isolates ofPestalotiopsis spp. were studied using four ITS primers (1&2, 4&5) ) and  SSR 1,2,4,5 and protein electrophoresis.