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The antifungal resistance in non-fumigatus <i>Aspergillus</i> spp., as well as <i>Aspergillus fumigatus</i>, poses a major therapeutic challenge which affects the entire healthcare community. Mutation occurrence of <i>cyp</i>51 gene paralogs is the major cause of azole resistance in <i>Aspergillus</i> spp. To obtain a full map of genomic changes, an accurate scan of the entire length of the <i>Aspergillus</i> genome is necessary. In this study, using whole genome sequencing (WGS) technique, we evaluated the mutation in <i>cyp51A</i>, <i>cyp51B</i>, <i>Cdr1B, AtrR, Hmg1, HapE</i> and <i>FfmA</i> genes in different clinical isolates of <i>Aspergillus fumigatus</i>, <i>Aspergillus niger</i>, <i>Aspergillus tubingensis</i>, <i>Aspergillus welwitschiae</i> and <i>Aspergillus terreus</i> which responded to minimum inhibitory concentrations of itraconazole above 16 µg mL⁻¹. We found different nonsynonymous mutations in the <i>cyp51A</i>, <i>cyp51B</i>, <i>Cdr1B</i><i>, AtrR, Hmg1, HapE</i> and <i>FfmA</i> gene loci. According to our findings, <i>Aspergillus</i> species isolated from different parts of the world may represent different pattern of resistance mechanisms which may be revealed by WGS.