The frequent use of antibiotics and chemicals by ornamental fish farmers causes health problems for both the fishes and the consumer. Therefore, the current study aimed to use environment- friendly materials as alternative therapeutic for some fungal diseases affecting ornamental fish Carassius auratus, using nano-chitosan gel and comparison its efficacy with that of pure chitosan gel. In the laboratory, the fungus was isolated from fish’s skin lesion and it identified morphologically and molecularly as Mucor circinelloides. Goldfish were experimentally infected with the fungus, and disease symptoms appeared ten days post infection. They were then treated with two types of ecofriendly compounds (pure chitosan gel and nano-chitosan gel) to compare their therapeutic efficacy. This study focused on evaluating the inhibitory efficacy of the fungus under in vitro conditions using three different concentrations of pure chitosan gel and Nano-chitosan gel (0.5%, 1%, and 2%). In vitro results demonstrated that nano-chitosan gel at 2% concentration achieved the highest inhibition zone (47.3 ± 3.2 mm), whereas pure chitosan gel at the same concentration reached 27.3 ± 2.1 mm (mean ± SD, n = 3). Statistical analysis using one-way ANOVA showed significant differences among treatments (P ≤ 0.05). Histological examinations of In vivo results demonstrated the activity of the nano-chitosan treatment in promoting the healing, with the epidermis, dermis, and muscle layers returning to their normal state within a shorter timeframe compared with pure chitosan gel treatment. Therefore, it can be concluded that nano-chitosan gel represents a promising, more efficient, and environment- friendly treatment option for fungal skin infections in ornamental fish. The isolation and registration of the fungus. M. circinelloides as a fish pathogen is for the first record in Iraq and it is registered at the National Center for Biotechnology Information (NCBI) under accession number LC904069.