Two isolates of Cucumber mosaic virus (CMV) originated from lily plants, named Ly2-CMV and Ly8-CMV, were compared with their pathological features in several host plants. Ly2-CMV and Ly8-CMV could induce systemic mosaic symptom in Nicotiana benthamiana, but Ly2-CMV could not systemically infect tomato and cucumber plants that have been used for CMV-propagative hosts. While Fny-CMV used as a control infected systemically the same host plants, producing typical CMV symptoms. Ly8-CMV could infect systemically two species of tobacco (N. tabacum cv. Xanthi-nc and N. glutinosa) and zucchini squash (Curcubita pepo), but Ly2 failed systemic infection on these plants. As resulted from tissue-print immunoblot assay, different kinetics of systemic movement between Ly2-CMV and Ly8-CMV were crucial for systemic infection in tobacco (cv. Xanthi-nc). Sequence analysis of full-length genome of two lily isolates showed Ly2 and Ly8 belonged to subgroup IA of CMV. The lily isolates shared overall 98% sequence identity in their genomes. Coat protein, 3a protein, and 2b protein involved in virus movement was highly conserved in genomes of the isolates Ly2 and Ly8. Although there is the low frequency of recombinants and reassortants in natural CMV population, phylogenetic analysis of each viral protein among a number of CMV isolates suggested that genetic variation in a defined population of CMV lily isolates was stochastically produced.