Penicillium is one of the most abundant components of soil fungal flora around the world. Several studies have been conducted on Penicillium identification to date,but most of them were associated with classical methods and morphological studies. In this investigation, more than fifty of soil samples from different provinces of Iran were collected and examined with soil suspension culture. Among various fungi, only Penicillium was selected. The pure cultures were prepared on PDA slants. Total DNA of isolates was extracted after culture in PDB media and was amplified with ribosomal region primers, ITS4 and ITS5,then were sequenced. Results of obtained sequences were compared with sequences exist in GenBank and these species were identified: Penicillium aculeatum, P. aurantiogriseum, P. chrysogenum, P. citrinum, P. commune, P.crustosum, P.pinophilum, and P. simplicissimum. Molecular identification of soil inhabitant Penicillia is a rapid method for accurate assessment of these fungal populations.