Abstract:[Background] The majority of studies on microbial contamination in drinking water focuses on bacteria, viruses, protozoa and worms, but less on fungi. We should also pay attention to fungi that contains a variety of potential pathogenic groups. [Objective] To study the changes in population and community structure of fungi and potential pathogenic fungi that may exist in urban water supply systems. [Methods] Two culture media (MEA and RB) were used to study the raw water, the purified water from two waterworks and the tap water from different secondary water supply modes in water supply systems. The total DNA of the above samples was extracted and the Illumina Miseq platform was used for high-throughput sequencing of the ITS1 gene. [Results] According to the high-throughput sequencing data, 579 470 effective sequences and 1 260 OTUs were obtained from 15 samples. The 228 fungal genera belong to 67 orders, 26 classes, and 8?phylum. The dominance of Ascomycota in water supply systems and fungal genera such as Aspergillus and Acremonium were present in all samples but rest were varied from samples to samples. The results of culture dependent and high-throughput sequencing showed that the population and species richness of fungi rose after filtering by biological activated carbon. Chlorination had a significant effect on the quantity, diversity and community of fungi. After passing through the water distribution systems and secondary water supply facilities, tap water sample showed significantly higher data in the quantity and species richness of fungi than effluent water. [Conclusion] The dominant fungi in the water supply system belong to Ascomycota and the dormant fungal spore can penetrate the multi-stage barriers in the water treatment process. The water purification process can effectively remove culturable fungi from water, and the biological activated carbon filtration process can lead a fungus leakage. Water supply pipelines and secondary water supply facilities are important sources of fungal contamination in drinking water and potentially pathogenic fungi that can cause infections exist in water supply systems.