Pdr5p-like ABC transporters play a significant role in azole resistance in Saccharomyces cerevisiae and Candida spp. Most of filamentous fungal species have multiple Pdr5p homologues. In this study, phylogenic analysis identified that filamentous fungi have at least two phylogenically distant groups of Pdr5p homologues. One contains PMR1-like Pdr5p homologues while the other contains both AtrF-like and AtrB-like Pdr5p homologues. Neurospora crassa has a total of four genes encoding Pdr5p homologues including CDR4 (PMR1-like), ATRB (AtrB-like), and ATRF (AtrF-like) and ATRF-2 (AtrF-like). By analyzing the susceptibilities of their knockout mutants to azole drugs including ketoconazole, fluconazole, and itraconazole, we found that deletion of cdr4 increased the susceptibility to antifungal azoles. In contrast, neither single-gene nor triple-gene deletion of atrb, atrf, and atrf-2 could not alter the susceptibility to azoles. In addition, cdr4, but not other Pdr5p homologue-coding genes, responded transcriptionally to ketoconazole stress. Together with the previous findings in other fungal species, these results suggest that the PMR1-like but not the AtrF-like or AtrB-like Pdr5p homologues play a key role in antifungal azole resistance in filamentous fungi.