A study of the mycoflora of three fish species: Lutjanus agennes (Red Snapper), Mugil cephalus (Mullet), Chrysichthys walkeri (Catfish) smoke-dried using Rubber wood (Hevea brassillensis) was carried out. Fish samples were bought from Ogbe-Ijoh market in Warri, Delta State and smoked using a traditional rectangular mud kiln (Chorkor) and stored on open benches in the laboratory at room temperature. Samples from the smoke-dried fish species were assessed tri-weekly using amended potato dextrose agar during the period of storage. Moisture content of the fish samples varied with storage time but was not significant (P> 0.05). The highest mean fungi count of (1.08 x10 , 8.0 x 10 5 and 1.16 x 10 6) cfu/g was recorded in the gills, muscle and skin of Chrysichthys walkeri during the six weeks of storage. There were significant differences (P<0.05) in the mean fungi counts in the three anatomical parts among the fish species. The predominant fungi species isolated from three different anatomical parts of smoke-dried fish samples during storage was made up of six (6) genera of fungi. Saccharomyces (37.69%), followed by Penicillum italicum (20.29%), Penicillum oxalicum (17.39%), Mucor sp (10.15%), Rhodotorula sp (7.25%), Aspergillus sp (5.79). The study has shown that fish samples could still be consumed after six (6) weeks of storage but were heavily contaminated with microorganisms and could pose a serious health concern for consumers.