Striped catfish (Pangasianodon hypophthalmus) is a very common aquaculture species in large scale throughout the Mekong Delta in Viet Nam for recent years. Disease occurrence caused by pathogens during culture period has been experienced. Fungi are more seriously and increasingly important pathogen in farmed striped catfish. In this study, the distribution of fungi in farmed catfish and farm water column in Mekong Delta was carried out. The results showed that most fungi were isolated from the water samples (269 isolates) rather than from farmed catfish (129 isolates). Seven fungal genera of Aspergillus, Fusarium, Acremonium, Trichoderma, Penicillium, Culvuclaria and Achlya were identified from the samples. Fusarium, Aspergillus, and Penicillium were dominating among identified fungi, while Culvuclaria was only identified from catfish samples. Moreover, water qualities of cultured ponds were suitable for the habitat of the fungi and surviving of cultured catfish. The study provides basic knowledge of the ecological distribution of fungi in the culture system of striped catfish in Mekong Delta, Viet Nam.