Badnaviruses are members of the Caulimoviridae family. They infect a range of important tropical crops such as banana (Banana streak virus, BSV), yam (e.g Dioscorea alata bacilliform virus, DaBV) and cocoa (Cocoa swollen shoot virus, CSSV), causing significant yield losses in numerous developing countries. BSV genomic sequences can integrate into Musa balbisiana chromosomes. This general class of sequences are referred to as endogenous pararetroviruses (EPRVs). BSV EPRVs can, after activation by various biotic and abiotic stresses such as genetic crosses or in vitro culture, result in episomal infectious particles. Such processes currently hamper the movement of banana plants harbouring EPRVs, because we are unable to evaluate their potential for disseminating BSV. Our data show that badnavirus-derived EPRVs appear widespread amongst some crops, which has serious implications for numerous germplasm conservation and plant genetic improvement programmes. Developing PCR-based methods for the detection of pathogenic EPRVs as well as episomal viral sequences is important for controlling badnaviruses and also for collecting much needed epidemiological data. We have designed versatile and strain-specific tools for the detection of badnaviruses, and carried out phylogenetic analyses of the diversity of BSV, CSSV and DaBV strains originating from various geographical locations, with regard to EPRVs and recombination. Our results show that these badnaviruses display very extensive generic diversity, making the development of molecular detection strategies to meet current regulations for the safe movement of germplasm difficult. They also provide data on the epidemiology of such viruses and onl their evolutionary status.