Geminiviruses are ssDNA viruses that infect a range of economically important crop species. We have developed a pathogen-derived transgenic approach to generate high levels of resistance against these pathogens in a susceptible cultivar of cassava (Manihot esculenta). Integration of the AC1 gene (which encodes the replication-associated protein) from African cassava mosaic virus imparted resistance against the homologous virus and provided strong cross-protection against two heterologous species of cassava-infecting geminiviruses. Short-interfering RNAs specific to the AC1 transgene were identified in the two most resistant transgenic plant lines prior to virus challenge. Levels of AC1 mRNA were suppressed in these plants. When challenged with geminiviruses, accumulation of viral DNA was reduced by up to 98% compared to controls, providing evidence that integration of AC1 initiates protection against viral infection via a post-transcriptional gene silencing mechanism. The robust cross-resistance reported has important implications for field deployment of transgenic strategies to control geminiviruses.