Adaptation to changes in the environment is crucial for the viability of all organisms. Although the importance of calcineurin in the stress response has been highlighted in filamentous fungi, little is known about the involvement of ion-responsive genes and pathways in conferring salt tolerance without calcium signaling. In this study, high-throughput RNA-seq was used to investigate salt stress-induced genes in the parent, ?cnaB, and ?cnaB?cchA strains of Aspergillus nidulans, which differ greatly in their salt adaption under salt stress. In total, 2,884 differentially expressed genes including 1,382 up- and 1,502 down-regulated genes were identi?ed. Secondary transporters, which were up-regulated to a greater extent in ?cnaB?cchA than in the parent or ?cnaB strains, are likely to play important roles in response to salt stress. Furthermore, 36 genes were exclusively up-regulated in the ?cnaB?cchA mutant under salt stress. Functional analysis of differentially expressed genes revealed that genes involved in transport, heat shock protein binding, and cell division processes were exclusively activated in ?cnaB?cchA. Overall, our findings reveal that secondary transporters and stress-responsive genes may play crucial roles in salt tolerance to bypass the requirement for the CchA-calcineurin pathway, contributing to a deeper understanding of the mechanisms that influence fungal salt stress adaption in Aspergillus. Overall design: mRNA profiles of wild type (WT), ?cnaB, and ?cnaB?cchA strains of Aspergillus nidulans treated with or without NaCl were generated by deep sequencing