A total of 34 species belonging to 21 genera of fungi were recorded on passion fruits of both pure and hybrid origin in Uganda, however, the pure type exhibited wider spectrum (28 species and 16 genera) than the hybrid type (21 & 15). Also, yeasts (unidentified and Rhodotorula mucilaginosa) were also encountered in high numbers. Moreover, the mean count of all mycobiota obtained from the pure type was higher than that of hybrid, despite the bigger size of the later. Members of yeasts and Cladosporium followed by Phoma, Penicillium, Fusarium and Alternaria species dominated on passion fruits of pure origin, while only C. cladosporioides, F. solani and yeasts dominated on the hybrid type. Treatment with Na-hypochlorite exhibited inhibitory effects on the total mycobiotic propagules as well as the dominant species from fruits of both types. The current results, therefore, suggest the use of Na-hypochlorite to control the post-harvest mycobiota associated with passion fruits. Regarding the mycobiota contaminating passion juice, yeasts were found to be the major contaminants with Candida parapsilosis being the most common. Moulds constituted only a minor proportion with Acremonium strictum followed by Fusarium chlamydosporum, F. moniliforme, F. acuminatum and F. solani as the most dominant species. In the heat-treated juice samples, the counts of the most commonly encountered mycobiota (both yeasts and molds) were significantly inhibited or completely eliminated. Some unidentified Bacillus species were also recovered from the juice, however, their counts in the heated samples were increased but insignificantly.