Viral diseases in Lilium spp. affect the bulb yield and cut flower quality. The main viruses found in Lilium are Lily symptomless virus (LSV), Lily mottle virus (LMoV) and Cucumber mosaic virus (CMV). The aim of the present study is the molecular characterization of LSV, LMoV and CMV in Lilium spp. from Argentina based on the coat protein gene sequence, and the classification of CMV into subgroup I or II. Lily samples were evaluated by both Double-antibody sandwich enzyme-linked immunosorbent assay (DAS-ELISA) and Reverse transcription polymerase chain reaction (RT-PCR). Infected plants showed amplicons of the expected size. RT-PCR allowed virus detection in three DAS-ELISA-negative plants. The PCR products were sequenced, and the nucleotide sequences were compared with available sequences from the GenBank (NCBI, National Center for Biotechnology Information). The LSV, LMoV and CMV strains showed high similarity percentages in the nucleotide and amino acid sequences of the capsid protein with isolates from different countries. The phylogenetic analysis showed that the Argentinian CMV strains found in lily belong to subgroup Ia.