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Knowledge of the genetic diversity detected among fungal species belonging to the genus <i>Aspergillus</i> is of key importance for explaining their important ecological role in the environment and agriculture. The current study aimed to identify <i>Aspergillus</i> species occurring in the rhizosphere of sugarcane in the South of Iran, and to investigate their mycotoxin profiles. One-hundred and twenty-five <i>Aspergillus</i> strains were isolated from the soil of eight major sugarcane-producing sites, and were molecularly identified using sequences of partial -tubulin (<i>benA</i>) and partial calmodulin (<i>CaM</i>) genes. Our molecular and phylogenetic results showed that around 70% of strains belonged to the <i>Aspergillus</i> section <i>Nigri</i>, and around 25% of species belonged to the <i>Aspergillus</i> section <i>Terre</i><i>i</i>. Species belonging to both sections are able to produce different mycotoxins. The production of mycotoxins was measured for each species, according to their known mycotoxin profile: patulin (PAT) and sterigmatocystin (STG) for <i>Aspergillus</i><i> </i><i>terreus</i>; ochratoxin A (OTA) and fumonisins for <i>Aspergillus</i> <i>welwitschiae</i>; and OTA alone for <i>Aspergillus</i><i> </i><i>tubingensis</i>. The data showed that the production of OTA was detected in only 4 out of 10 strains of <i>A. </i><i>welwitschiae</i>, while none of the <i>A. </i><i>tubingensis</i> strains analyzed produced the mycotoxin. Fumonisins were produced by 8 out of 10 strains of <i>A. </i><i>welwitschiae</i>. Finally, none of the 23 strains of <i>A. </i><i>terreus</i> produced STG, while 13 of them produced PAT. The occurrence of such mycotoxigenic plant pathogens among the fungal community occurring in soil of sugarcane fields may represent a significant source of inoculum for the possible colonization of sugarcane plants, since the early stages of plant growth, due to the mycotoxin production capability, could have worrisome implications in terms of both the safety and loss of products at harvest.