This study aimed to investigate the fungal species isolation and confirmation by the Multiplex PCR method in aquatic fish. Evaluation of the inhibitory effect of nano-essential oils of Carum copticum on isolated fungal species was also conducted in this study. The PCR results showed that 3 out of 5 samples were diagnosed with Fusarium solani, and two of them were positive for Saprolegnia. Moreover, in 0.1% of the females' nanoparticles, one peak appeared that showed a particle with an average diameter of 360 nm, and two nanoparticles showed a peak with a mean diameter of 242 nm. The results of minimum inhibitory concentrations (MIC) and minimum fungicidal concentrations (MFC) showed that 0.01% nano essential oil had 0.08 and 0.07 mg/ml MIC values against Fusarium solani and Saprolegnia, respectively. Gram/ml was on the growth of Fusarium solani species. The essential oils of female plants had an MIC of 0.07 in 0.1% essential oil and 0.03 mg/ml in 0.01% essential oil in Saprolegnia. Furthermore, in the case of 0.1% nano essential oil, the results showed the MIC values of 0.04 and 0.03 mg/ml against Fusarium solani and Saprolegnia, respectively. The MFC values of 0.1% nano essential oil were 0.1 and 0.07 mg/ml against Fusarium solani and Saprolegnia, respectively. It was not found on Fusarium and Saprolegnia. Overall, the results of this study using PCR for direct detection showed that 70% and 50% of the samples were Fusarium solani and Saprolegnia positive, respectively; therefore, the PCR was an efficient method for the detection of fungi. According to the results of nano-essential oil (0.1%) of females, this nano-essence had a strong inhibitory effect on Fusarium solani and Saprolegnia.