The occurrence of fungi in drinking water systems has received increased attention over recent decades and fungi are now generally accepted as drinking water system contaminants. However, fungal contamination of bottled water has received little attention. Forty unopened bottled water samples, of different trademarks, were collected from various localities in Jeddah city, Saudi Arabia and analyzed for fungal contamination: (1) immediately after opening the bottles; and (2) after closing and storing them for 180 and 365 days. The fungal species were identified under a compound microscope followed by molecular sequencing. At least one fungal species were found in 58% of the bottles. In total, 18 fungal species belonging to 11 fungal genera were identified. Rhizopus nigricans and seven different species of Aspergillus were found to frequently contaminate the bottled water samples. Penicillium sp. were found in one sample. The 180 days storage of opened and reclosed bottles did not substantially affect the abundance of fungi or the species found. Some of the fungi identified may be pathogenic and the contamination of fungi in bottled water should be considered during the processing of water.