The purpose of this study is to investigate the intra- and inter-specific genetic relationship of some strawberry- and orange-associated fungi based on DNA markers technique. Five fungal isolates belonging to three different genera were isolated from strawberry and orange samples. The isolates were morphologically characterized as Aspergillus fumigatus, which originated from orange samples; A. flavus and A. niger, both originated from strawberries; and Rhizopus stolonifer and Alternaria alternata, both originated from orange samples. The five fungal isolates were subjected to investigating intra- and inter-specific genetic relatedness, employing the technique of random amplified polymorphic DNA-polymerase chain reaction (RAPD-PCR) marker using ten oligonucleotide primers. The RAPD-PCR analysis revealed a high interspecific relationship between the three Aspergillus species and Rhizopus stolonifer, as well as Alternaria alternata. It also revealed a high intraspecific genetic relationship between A. fumigatus and A. flavus, which were isolated from different environments, surpassing the observed relationships between A. flavus and A. niger, which were isolated from the same environment. This finding confirms genetic homogeneity within the studied Aspergillus species, suggesting a potential for molecular identification of genetic diversity among different individuals in the Aspergillus genus, taking into consideration their respective origins.