The genus Cladosporium Link is one of the largest genera of hyphomycetes and members of this genus have worldwide distribution. During recent decade, molecular studies have led to introduction of new species and combinations in the genus Cladosporium. This study was carried out for phylogenetic analysis of some Iranian isolates of the genus Cladosporium. In this study, 105 sequences (including 82 sequences from Cladosporium cladosporioides s. l., C. sphaerospermum s. l. and C. herbarum s. l. and 32 sequences obtained from GeneBank) were used in phylogenetic analysis. The data analyzed using Neighbor-joining (NJ), Minimum-Evolution (ME) and Maximum-parsimony (MP) methods in MEGA 5.0 software. The results showed that ITS region could not differentiate closely related or cryptic species in the genus Cladosporium, and all isolates of C. cladosporioides s. l. and C. herbarum s. l. were placed in one clade by ITS. On the other hand phylogenetic analysis of EF1-α sequences showed much better resolution for several species. However, there are still several isolates of the complex species such as C. cladosporioides, C. perangustum, C. pseudocladosporioides and C. tenuissimum that are morphologically indistinguishable but are phylogenetically clustered in several subclades.