Two isolates of brown root disease fungi were obtained from diseased roots of sentang (Azadirachta excelsa). Morphological characters from macroscopic and microscopic studies suggested that both isolates were from the same genus namely Phellinus noxius and Phellinus sp. Cloning and sequencing of ITS region were conducted to investigate further the variation between the two species at
molecular level. PCR-amplified ITS regions were cloned in pCR2.1 and sequenced. DNA sequences sized 723bp and 710bp were obtained for Phellinus noxius and Phellinus sp respectively. Comparison between the two sequences showed 98% similarity where three nucleotide substitutions and three insertion/deletion regions were found sized 8bp, 2bp and 3bp respectively.