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Background: Sugarcane smut is a disease that is caused by the fungus Sporisorium scitamineum. This is a disease of economic importance in the sugarcane industry, because it can cause losses of up to 50%. Current management practices have shown to be ineffective in controlling the fungal disease and hence there is the need for the development of antifungal agents that are biocompatible, non-toxic, environmentally friendly and easy to develop. Biosynthesized silver nanoparticles have been found to possess antimicrobial properties, and have not been explored on S. scitamineum. Results: The synthesis of silver nanoparticles using Carissa spinarum yielded particles that were spherical, smooth and they had a size range from 3nm to 33nm in size. Optimization of the mixtures using ultraviolet-visual spectroscopy (UV-Vis) showed peaks in the range of 340nm to 450nm. The Fourier transform infrared spectroscopy analysis identified proteins to be essential capping agents and reducing sugars were responsible for the reduction of the silver nitrate to nanoparticles and stabilizing the nanoparticles. The biosynthesized silver nanoparticles had the highest antifungal activity at 5mg/ml, while the minimum inhibitory concentration and minimum fungal concentration were 78µg/ml. The in-vivo assays showed a significant (at P=0.05) reduction of the pathogen biomass concentration on the plants that were treated with the nanoparticles when compared to the control plants. The application of 58.5µg/ml of the b-AgNPs to the S. scitamineum resulted to a significant (P=0.05) increase in expression of the bE and bW genes, while the treatment with 39 µg/ml significantly (P=0.05) increased the expression of the bE gene, but had no significant (P=0.05) change in the expression of the bW gene. Conclusion: Silver nanoparticles that were synthesized successfully using C. spinarum crude extract inhibited the growth of S. scitamineum both in-vitro and in-vivo. The silver nanoparticles had a regulatory effect on the expression of the bE and bW genes in the fungus.