Garlic and onion grown in Indian Punjab are usually infected with several viruses including the common allium viruses of the genera Allexivirus, Potyvirus and Carlavirus. Onion Yellow Dwarf Virus (OYDV), Shallot Latent Virus (SLV) and Garlic Virus D (GarV-D) were indentified by RT-PCR assay using virus-specific primer sets. BLASTn analysis of sequences confirmed the presence of OYDV and GarV-D, SLV in infected onion and garlic samples, respectively. During BLASTn analysis OYDV isolate (KP862051) shared 98-99% identity with OYDV isolates (KP862053, KP862052) from Ludhiana and 97% similarity with OYDV isolate (FR833734) from New Delhi. Whereas in the case of garlic viruses, SLV (KR074209) had 91% similarity to SLV isolate (EF600902) from New Delhi and GarV-D isolate (KR045606) showed a maximum resemblance of 99% with GarV-D isolate (HQ724840) from Spain. OYDV isolate (KP862051) shared 79% nt identity with Rajasthan isolate (EU045556) and 72.9% with New Delhi isolate (FR873734), GarV-D isolate (KR045606) shared maximum 99.5% nt similarity with Spain isolate (HQ724840) and SLV isolate (KR074209) shared 90.8 nt similarity with New Delhi isolate (EF600902). Phylogenetic analysis of nucleotide sequences revealed that Indian isolates of OYDV and GarV-D have significantly the closest phylogenetic relationship with Indian and abroad isolates, however SLV isolate (KR074209) was found significantly divergent from abroad isolates. Phylogenetic analysis confirms the evolutionary origin of OYDV and SLV from Indian ancestors and GarV-D origin from Spain isolates. Present investigation unravels the virus diversity, subgrouping, evolutionary history within the allium viruses in India.