Abstract Background Tomato mosaic virus (ToMV) is a dangerous disease of tomato (Lycopersicon esculentum) that reduces dramatically the yield. To reduce ToMV infection, microalgal isolates were utilized. Microalgal species (Chlorella vulgaris, Anabaena oryzae, Spirulina platensis, Nostoc linckia and Dunaliella salina) were shown to be responsible for the stimulation of tomato resistance against ToMV. Results Initial signs of discoloration and mosaic in ToMV-inoculated plants were detected and identified on inoculated leaves at 6 and 12 dpi in control and treated plants, respectively, suggesting that microalgae may inhibit ToMV growth. Treatment with microalgae resulted in a significant decrease in symptoms (up to 63% reduction in disease severity) and negative ELISA readings, indicating that the microalgae induced resistance in tomato against ToMV infection. The isolates also enhanced the activity of pathogenesis-related enzymes (PPO and POX reaching to 0.033 and 0.054 in D. salina, respectively), as well as tomato growth characters in comparison with the control. Microalgal treatments demonstrated that the salicylic acid (SA) and jasmonic acid (JA) pathways were involved in tomato plant defense responses. The relative gene expressions of PR1 and phenylalanine ammonia lyase (PAL), which are involved in the SA and JA pathways, respectively, were improved in treated plants compared to the control. Conclusion The findings indicated that algal-induced ToMV resistance was mediated via several defense pathways in tomato. The antiviral mechanism was described, which provides a light on the potential of algae in plant viral disease management.