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Lotus (Nelumbo nucifera Gaertn.) is an economically important perennial aquatic herb plant in China. Presently, viral diseases caused by Cucumber mosaic virus (CMV) and Dasheen mosaic virus (DsMV) are detected in lotus. In this study, the putatively novel badnaviruses from lotus plants (LBVs) were identified using next-generation sequencing of siRNAs and conventional Sanger sequencing based on the RT/RNase H coding region sequences. Lotus plants infected by LBVs harbored virus quasispecies. A unique recombination event of LBVs was found in a single lotus plant. Sap inoculation showed that LBVs could actively replicate in the lotus plants, but without a wide host range. The field survey of 43 lotus plants in Jiangsu Province showed a prevalence of 62.8％for LBVs, confirming that it is widely distributed in Jiangsu Province of China.