Viruses cause destructive and economically important diseases on plantain and banana worldwide. They also hamper the exchange and diffusion of Musa germplasm. Most reported viruses infecting plantain and banana are transmitted vegetatively or by biological vectors and can therefore be managed through the control of such vectors. Meanwhile, Banana streak virus (BSV) is either transmitted by mealybugs or through stress-induced activation processes of viral sequences integrated into the genome of Musa balbisiana. Therefore its control is much more challenging. Innovative and sensitive methods have been developed and implemented for the detection and control of two viruses infecting banana and plantain, Banana Mild Mosaic Virus (BanMMV) and BSV. They are now used routinely for the safe mass production of certified Musa germplasm. Meanwhile, recent breakthrough on the activation of BSV sequences in natural or created plantain hybrids following in vitro mass propagation have been registered, leading to new recommendations for a better control of BSV.