Nineteen identified species which belong to nine fungal genera were recovered from 14 samples collected from different sites of the Red Sea governorate. The aquatic fungal genera were Allomyces, Dictyuchus, Saprolegnia and Pythium while, the terrestrial fungal genera were Aspergillus, Penicillium, Fusarium, Neurospora and Rhizopus. Aspergillus was the most frequent genus, represented by seven species, of which A. niger, A. flavus and A. ustus were the most common. Penicillium was of occurred less frequently and was represented by two species, while Fusarium was isolated unfrequently and contributed four species. The remaining genera were unfrequent or rare and were each represented by one species. In addition, two electrophoretic isozyme patterns, esterase and glutamate oxalate transaminase (GOT), were determined to measure variability among 10 isolates of Fusarium. The results revealed that the tested fungi differed from each other in one or more esterase bands, except that F. moniliforme isolated from Safaga and from 40 Kilometers south of El-Kaussier yielded similar banding pattern. The activity of GOT was observed in the samples of F. solani and F. oxysporum and not detected in other isolates of Fusarium. The results indicated that F. solani differed from F. oxysporum in the isozymes of GOT, while no differences were observed between the isolated of the same species.