​Allium plants are affected by different pathogens, including viruses. These viruses cause significant yield losses and consider difficult to control because of the lack of chemical treatment for the target virus. The next-generation sequence (NGS) technology was used to discover unknown or multiple viruses in garlic plants.  In the present work, we tested garlic for the presence of onion yellow dwarf virus (OYDV), leek yellow-strip virus (LYSV),  garlic common latent virus (GarCLV), garlic virus X and iris yellow spot virus (IYSV), from different parts of plants as leaves and bulbs collected from different garlic production. regions in Jordan, using molecular tests such as RT-PCR and NGS. Deep sequencing revealed the presence of OYDV, LYSV, GarCLV and GVX  for the first time in Jordan.