The economic losses due fungal infection in Siberian sturgeon hatcheries and the side effects of malachite green consumption on the consumer and environment is very important. Therefore, it is essential to investigate and introduce the suitable substitute natural substances instead of malachite green. The aim of this study was to compare the antifungal effect of alcoholic extract T. vulgris with malachite green on fungus isolated from Siberian sturgeon eggs. Sampling was done in the reproductive seasons of A.baerii. The samples were inoculated in culture media (SDA) and glucose-peptone agar at a temperature that similar to the temperature at hatchery (25 °C) for 5-7 days and then isolated fungus was identified. The antifungal effect of the T. vulgris extract was evaluated by disk diffusion method and the minimum inhibitory concentration (MIC) and minimum fungicidal concentration (MFC) of fungus were measured. In this study, Saprolegnia sp., Fusarium sp., Rhodotorula sp., Penicilium sp., Trichoderma sp., Chrysosporium sp. and Strile hyphae sp. was isolated and identified from fertilized eggs of A.baerii. According to the results, T. vulgris extract has a significant effect on the number of the all isolated fungal species (P<0.05) the most effect was observed on Saprolegnia and the least effect on Fusarium sp. and Trichoderma sp. The MIC value of alcoholic extract for Saprolegnia sp., Fusarium sp., Rhodotorula sp., Penicilium sp., Trichoderma sp., Chrysosporium sp. and Strile hyphae sp. was ≥0.75, 3, 1.5, 1.5, 0.75, 1.5 and ≤0.75 mg/ml, respectively and MFC value for these fungus were determined as ≥1.5, ≥3, 3, 3, 1.5, 3 and 1.5 mg/ml, respectively. In general, due to the high frequency of Saprolegnia sp. fungi in A.baerii eggs, and the significant effect of alcoholic extract of T. vulgris, it could be used as a good alternative for malachite green to reduce the frequency of fungal contamination and its economic losses during reproductive seasons of A.baerii.