In order to clarify the virus infection of lily in production,virus-infected lily samples collected from Yunnan and Zhejiang Provinces were analyzed by using high-throughput sequencing technique.Eight known viruses，including lily mottle virus （LMoV），cucumber mosaic virus （CMV），plantago asiatica mosaic virus （PlAMV），dahlia mosaic virus （DMV），figwort mosaic virus （FMV），rose yellow vein mosaic virus （RYVV），dahlia common mosaic virus （DCMV），and cassava vein mosaic virus （CsVMV），and two new viruses were identified through sequence alignment and assembly.Then 48 lily samples collected from Yunnan，Zhejiang，Jiangxi，Shanghai，Guangdong and Hunan Provinces were detected using reverse transcription polymerase chain reaction （RT-PCR）.The results showed that DMV，RYVV，PlAMV and LMoV were predominant and the positive detection rates of them were above 95%.The positive rate of FMV was higher than 85%，while that of CMV was the lowest，which was only positive in the samples from Kunming，Yunnan Province.DCMV and CsVMV were not detected in these samples.The mixed infection rate of lily virus was 100%，and 3-6 viruses were positive in a single sample，with a total of 6 mix types.The mixed infection of lily virus in Kunming，Yunnan Province was the most complicated.A single sample from Kunming was infected with 5-6 viruses.These results indicated that the detection rate and the mixed infection rate of lily viruses were both high in the detected areas. Therefore, it is necessary to monitor and detect the viruses that infected lily plants as early as possible to prevent the transmission of viruses and avoid economic losses.