Objective:To analyze the molecular characteristics of dengue virus (DENV) strains circulating in Shantou city in 2018 and 2019 for elucidating the reasons causing strikingly different dengue fever epidemics during the two years and understanding the transmission characteristics and routes of DENV, and to provide reference for the prevention and control of dengue fever.Methods:Detection of viral nucleic acid contents and amplification and sequencing of E gene were carried out on 872 samples positive for DENV acid in 2018 and 2019. Phylogenetic trees were constructed based on the E gene sequences to analyze the homology of DENV strains. The sources and transmission routes of the strains were also analyzed. Results:A total of 99 sequences of DENV E gene were acquired, including 68 DENV-1 sequences and 31 DENV-2 sequences. The cases of dengue fever were sporadic in 2018. Phylogenetic tree showed the strains isolated in 2018 were from multi-sources and closely related to those found in Guangzhou city and Southeast Asia area. Dengue fever outbreaks occurred in 2019 and most of the prevalent strains were from a single source, which was speculated to be Cambodia. Conclusions:Dengue fever in Shantou city was mainly caused by imported strains of the same year rather than by local strains in previous years. DENV strains in Shantou might be traced back to Southeast Asia area and transmitted to Shantou through many routes.