The present study aimed to compare the brain structure of 14 fish species with different ecological characteristics from the Persian Gulf. After precise dissection of the brain and weighing, fixation was performed using Bouin's solution, followed by tissue processing, embedding in paraffin, sectioning to a thickness of 12 μm, and staining with hematoxylin and eosin. Sections were observed under microscope and photographed to precisely describe the brain structures. The results showed that the grey bamboo shark (Chiloscyllium griseum) differed considerably in structure of the brain compared to bony fish, and it showed the highest brain-to-body mass ratio (0.8±0.02) (p<0.05). The crista cerebellaris and granular section were more obvious in the croaker (Otolithes ruber), maybe due to its well developed lateral line. A plankton-feeding shad, Tenualosa ilisha, had less brain-to-body mass ratio and a more simple structural brain compared to the narrow-barred Spanish mackerel (Scomberomorus commerson), which occupies the top of the food chain. Moreover, duskytail grouper (Epinephelus bleekeri), living in the coral reef ecosystem, had a greater brain-to-body mass ratio and more complex brain structure compared to flounders occupying a simpler environment. This study highlights that phylogenetics, trophic level, and complexity of environment have important relationships with brain anatomy of fishes in the Persian Gulf.