The GI tract of P. nigrolineatus is enriched with lignocellulose and provides a unique microenvironment. The fungal population within this fish warrants investigation to better understand their role in this process and possibly identify new lignocellulose degradation pathways and microbial interactions. The aim of the present study was to examine and compare the diversity of fungal communities in different GI tract regions as a function of diet. To our knowledge, this is the first description of fungal populations using molecular techniques in the GI tract of fish.