A DissertationFungal diseases are prevalent in fish and have the potential of limiting productivity in aquaculture. This study aimed to isolate and determine fungal infections in hatchery with female Rufiji tilapia and their hybrids of male Rufiji tilapia and female Nile tilapia. An experimental study design was conducted to determine the occurrence of fungal infections and to characterize the isolates of Aspergillus flavus and Aspergillus niger. Fish samples were randomly collected from the hatchery at the Institute of Marine Sciences Mariculture centre in Pangani. In the sampled fish the gills, gastrointestinal tract and skin were collected. The morphological and physiological tests were employed to isolate and identify fungi using SDA. The lactophenol detached crystal cotton blue was used for characterization of fungi. The Rufiji tilapia stocked at different salinities were infected by A. niger and A. flavus at 72.4 % and 17.1% (n = 61) respectively. The prevalence of A. niger and A. flavus in water of tilapia and hybrids was 37.4 % and 10.6% respectively. Rufiji tilapia and hybrids were infected by A. niger and A. flavus at 37.9 % and 6.5 % (n = 62) respectively. For PCR based analysis, fragments of bp400 and 895 were detected for A.flavus and bp290 for A.niger. Despite the percentage variations for fungal isolates in some of the fish, overall, there was a significant (P0.05) reduction of prevalence of fungal infections with increasing salinities. In the hybrids, an increase in salinity did not influence the prevalence of Aspergillus species (P0.05). Increase in salinity has no influence on the growth of A. flavus in fish organs of Rufiji tilapia. Conventional methods are time-consuming and less sensitive; PCR methods provide more specification and high sensitivity of the target organism. Different salinities of 15, 25 and 35 are potential for mariculture since they cannot support the existence of A. niger unlike A. flavus, which showed significant difference in fish organs.