Nine Penicillium digitatum isolates were isolated from citrus fruits and tested for their pathogenicity on Navel orange fruit (Citrus sinensis L.). In this regard, the isolates exhibited three different levels of virulence. The isolates were identified morphologically using malt extract agar (MEA) and Czapek yeast extract agar (CYA) for colony characteristics, and MEA for microscopic features. Each one of the isolates has the unique features of P. digitatum, especially the largest conidia (6.1-11.9 µm long X 3.2-8 µm width), and phialides (10.1-21.4 µm long X 4-5.1 µm width). In addition, the isolates were identified on a molecular basis using ITS1 and ITS4 primers to confirm morphological identification. Phylogenetic analysis revealed that there was high variance among the isolates, and there were different relations between some of our isolates and other P. digitatum registered strains originating from different countries all over the world. The sequences were submitted to respective GenBank nucleotide databases with accession No. OR198852, OR198853, OR198854, OR198855, OR198856, OR198857, OR198858, OR198859 and OR198860. We also isolated a new P. digitatum (OB15: OR198859) strain with high virulence and rapid sporulation