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Aspergillus fumigatus causes a range of human and animal diseases collectively known as aspergillosis. A . fumigatus possesses and expresses a range of genetic determinants of virulence, which facilitate colonisation and disease progression, including the secretion of mycotoxins. Gliotoxin (GT) is the best studied A . fumigatus mycotoxin with a wide range of known toxic effects that impair human immune cell function. GT is also highly toxic to A . fumigatus and this fungus has evolved self-protection mechanisms that include (i) the GT efflux pump GliA, (ii) the GT neutralising enzyme GliT, and (iii) the negative regulation of GT biosynthesis by the bis -thiomethyltransferase GtmA. The transcription factor (TF) RglT is the main regulator of GliT and this GT protection mechanism also occurs in the non-GT producing fungus A . nidulans . However, the A . nidulans genome does not encode GtmA and GliA. This work aimed at analysing the transcriptional response to exogenous GT in A . fumigatus and A . nidulans , two distantly related Aspergillus species, and to identify additional components required for GT protection. RNA-sequencing shows a highly different transcriptional response to exogenous GT with the RglT-dependent regulon also significantly differing between A . fumigatus and A . nidulans . However, we were able to observe homologs whose expression pattern was similar in both species (43 RglT-independent and 11 RglT-dependent). Based on this approach, we identified a novel RglT-dependent methyltranferase, MtrA, involved in GT protection. Taking into consideration the occurrence of RglT-independent modulated genes, we screened an A . fumigatus deletion library of 484 transcription factors (TFs) for sensitivity to GT and identified 15 TFs important for GT self-protection. Of these, the TF KojR, which is essential for kojic acid biosynthesis in Aspergillus oryzae , was also essential for virulence and GT biosynthesis in A . fumigatus , and for GT protection in A . fumigatus , A . nidulans , and A . oryzae . KojR regulates rglT , gliT , gliJ expression and sulfur metabolism in Aspergillus species. Together, this study identified conserved components required for GT protection in Aspergillus species.