Fungi were isolated from fresh brown shrimps (Penaeus aztecus) purchased from three different markets in Port Harcourt using standard mycological methods. The total counts of heterotrophic fungi range from 2.0 x 104 spore forming units per gram (sfu/g) to 7.1 x 104 sfu/g, while the total counts for pathogenic fungi range from 1.7 x 104 sfu/g to 7.1 x 104 sfu/g. The heterotrophic fungi and their percentage occurrence in the H/E/T (head, exoskeleton and telson/uropod) before deterioration and about deterioration were: Aspergillus clavatus (20%), Aspergillus flavus (20%), Penicillium sp (20%), Rhizopus sp (20%), Rhodotorula sp (20%), and Aspergillus flavus (28.6%), Mucor hiemalis (14.3%), Penicilllium sp (14.3%), Rhizopus sp (14.3%), Rhizopus stolonifer (14.3%), Yeast sp (14.3%) respectively. While the pathogenic fungal occurrence before deterioration and about deterioration in the H/E/T were: Aspergillus clavatus (11.1%), Aspergillus flavus (22.2%), Penicillium sp (33.3%), Rhizopus oryzae (11.1%), Rhodotorula sp (11.1%), Yeast sp (11.1%), and Aspergillus clavatus (12.5%), Aspergillus flavus (12.5%), Mucor hiemalis (12.5%), Penicillium sp (12.5%), Rhodotorula sp (12.5%)and Yeast sp (37.5%) respectively. Heterotrophic fungi in the flesh before deterioration and about deterioration were, Aspergillus flavus (33.3%), Penicillium sp (33.3%), yeast sp (33.3%) and Aspergillus flavus (22.2%), Aspergillus niger (11.1%), Mucor plumbeus (11.1%), Penicillium sp (22.2%), Phialophora fastigiata (11.1%), Rhizopus stolonifer (11.1%) and Rhodotorula sp (11.1%) respectively. While the pathogenic fungal occurrence before deterioration and about deterioration in the flesh were Aspergillius flavus (28.6%), Penicillium sp (14.3%), Rhizopus oligosporus (28.6%), Rhizopus stolonifer (14.3%), Yeast sp (14.3%), and Aspergillus niger (10%), Mucor hiemalis (10%), Mucor plumbeus (20%), Penicillium sp (10%), Rhizopus stolonifer (10%), Rhodotorula sp (20%), and Yeast sp (20%) respectively. The presence of these fungi in the shrimps is attributed to contamination from the environment and from shrimp handlers (mongers). Also, some of these fungi are normal flora of the shrimp which unfortunately happens to be opportunistic pathogens or pathogens of humans. The maintenance of high personal and environmental hygiene as well as proper heating and cooking will improve fresh shrimp quality and prevent food-borne diseases.