The rapid and global emergence of azole resistance in the human pathogen Aspergillus fumigatus has drawn attention. Thus, a thorough understanding of its mechanisms of drug resistance requires extensive exploration. In this study, we found that the loss of the putative calcium-dependent protein-encoding gene algA causes an increased frequency of azole-resistant A. fumigatus isolates. In contrast to previously identified azole-resistant isolates related to cyp51A mutations, only one isolate carries a point mutation in cyp51A (F219L mutation) among 105 independent stable azole-resistant isolates. Through next-generation sequencing (NGS), we successfully identified a new mutation (R243Q substitution) conferring azole resistance in the putative A. fumigatus farnesyltransferase Cox10 (AfCox10) (AFUB_065450). High-performance liquid chromatography (HPLC) analysis verified that the decreased absorption of itraconazole in related Afcox10 mutants is the primary reason for itraconazole resistance. Moreover, a complementation experiment by reengineering the mutation in a parental wild-type background strain demonstrated that both the F219L and R243Q mutations contribute to itraconazole resistance in an algAindependent manner. These data collectively suggest that the loss of algA results in an increased frequency of azole-resistant isolates with a non-cyp51A mutation. Our findings indicate that there are many unexplored non-cyp51A mutations conferring azole resistance in A. fumigatus and that algA defects make it possible to isolate drug-resistant alleles. In addition, our study suggests that genome-wide sequencing combined with alignment comparison analysis is an efficient approach to identify the contribution of single nucleotide polymorphism (SNP) diversity to drug resistance.KEYWORDS Aspergillus fumigatus, azole resistance, cox10, cyp51A, mutation T he filamentous fungus Aspergillus fumigatus, one of the major opportunistic fungal pathogens, causes invasive fungal infections (IFIs) among immunosuppressed patients, with a high mortality rate (1, 2). Currently, azole compounds are the primary clinical therapy drug for IFIs and have been widely used in agriculture as well (3, 4). However, with the emergence of azole-resistant isolates, the efficacy of azole antifungals has been restricted so that azole resistance is becoming a growing public health menace (5-8). Therefore, the identification of genes whose mutations lead to drug resistance can provide a complete understanding of the molecular mechanisms underlying azole resistance.Previous studies verified that the most common mechanisms of resistance to azole antifungals observed in A. fumigatus samples are due to Cyp51A mutations, which