The actual extent of fungal diversity in different environmental media is still a subject of ongoing research. Little is currently known about the diversity of fungal populations in industrial streams. This study characterized the fungal diversity of different industrial effluents using a high-throughput sequencing approach. A total of 234617 quality filtered reads were obtained from the collected wastewater samples. Phylogenetic taxonomy revealed that resident fungal communities were classified as 6 phyla, 31 classes, 79 orders, 144 families, and 192 genera. Ascomycota and Basidiomycota were the most dominant phyla whose relative abundance ranged from 23.29% to 38.31%, and 17.34% to 33.51%, respectively. Recovered operational taxonomic units (OTUs) ranged from 292 (Dixon) to 427 (Capegate). The existence of some fungal genera identified in the industrial wastewaters correlated to physicochemical variables and had the potential to play important roles in organic decomposition, pollutant degradation, and xenobiotic transformation. Meanwhile, the occurrence of unclassified fungal sequences (22.5% to 33.09%) suggests that these effluents are a potential reservoir of as-yet uncharacterized fungal species.