This study was conducted to quantify and characterize the mycoflora associated with the ‘green water’ culture system of Penaeus monodon. Samples of water, tilapia gut and mucus, and shrimp hepatopancreas from three shrimp farms were collected during 15, 30, 45 and 60 days of culture (DOC). Results showed that high fungal loads were observed in tilapia gut (total: 117–1352 colony forming unit (CFU) 5 cm hind gut−1; yeasts: 0–136 CFU 5 cm hind gut−1) and mucus (total: 12–311 CFU (5 cm2)−1; yeasts: 0–88 CFU (5 cm2)−1), while minimal fungal populations were observed in water samples (total: 0–110CFU mL−1; yeasts: 0–5 CFU ml−1). Shrimp hepatopancreas harboured a very low number of filamentous fungi (0–27 CFU 0.1 g−1) and yeasts (0–7CFU 0.1 g−1) especially at 60 DOC. The filamentous fungal isolates were dominated by Penicillium and Aspergillus species, while the yeast populations were dominated by Rhodotorula and Saccharomyces species. The dominance of these fungi on tilapia mucus and gut and their presence in the rearing water might play an important role in the overall mechanisms involved in the control of luminous Vibrio in the ‘green water’ grow-out culture of P. monodon.