This study investigates the potential application of plant-based resources with antimicrobial properties, namely hops (Humulus lupulus) and calendula (Calendula officinalis), as viable alternatives to commercial disinfectants for the prevention of fungal growth during the incubation period of rainbow trout (Oncorhynchus mykiss) eggs. Fertilized eggs were examined with daily 20-minute baths in 0.25 mg, 0.5 mg, and 1 mg concentrations throughout the incubation period (33-35 days). Control group, commercial formaldehyde, hops, and calendula groups were examined in triplicate for each concentration. As a result, the lowest hatching ratio was observed in the control group with 84.77%, while the hatching ratios in the other groups were as follows: commercial disinfectant group with 86.22%, hops group with 87.44% (0.25 mg), calendula group 88% with (0.25 mg), calendula group with 89% (0.5 mg), calendula group with 89.33% (1 mg), hops group with 89.55% (0.5 mg), and the highest hatching ratio was found in the hops group with 90.66% (1 mg). The lowest survival rate was observed in the control group with 85.22%, with the survival rates of the other groups were 86.44% in the commercial disinfectant group, 87.55% (0.25 mg) in the hops group, 88.55% (0.25 mg) in the calendula group, 88.88% (0.5 mg) in the calendula group, 89.33% (1 mg) in the calendula group, 89.55% (0.5 mg) in the hops group, and the highest survival rate was 90.11% (1 mg) in the hops group. In conclusion, it was specified that plant-based by-products (hops and calendula) could be used as alternative disinfectants to commercial chemicals in the disinfection of rainbow trout eggs and fry, and the most appropriate concentration was 1 mg.