Virus disease is one of the most serious diseases in tomato production in Hainan, China. The small RNA deep sequencing data of tomato virome in Hainan revealed the presence of Southern tomato virus (STV) in samples from several regions, and a single STV infected sample was found. RT-PCR screening of 987 field samples with virus-like symptoms collected from 2015 to 2021, was carried out to determine the distribution of STV in Hainan province. Results indicated that STV was detected in 142 samples from nine regions, STV had existed in Hainan tomatoes as early as 2015, STV detection rate increased from 8.82% in 2015 to 22.45% in 2021, showing an upward trend year by year. The complete genome length of four isolates amplified using RT-PCR and RACE was identical, each consisting of 3446 nt. Two partially overlapping open reading frames (ORFs) presented in the positive-sense RNA strand, the 5′-proximal ORF (position 147-1280 nt) encoded a 377 amino acid (aa) peptide representing a potential coat protein (p42), the second ORF (position 1048-3336 nt) contained typical motifs for an RNA-dependent RNA polymerase (762 aa). The length of 5′ untranslated region (UTR) and 3′ UTR was 146 nt and 110 nt respectively. Paired comparison showed that the nucleotide similarity among four STV isolates was 99.86%-100.00%, the nucleotide similarities with other STV isolates available in GenBank were 98.45%-99.94%. In phylogenetic trees based on the complete genome of STV, eighty STV isolates were obviously divided into two groups (Group Ⅰ and Group Ⅱ). Group Ⅰ included Asian, American, European and African isolates. In group Ⅱ, except for one Asian isolate, the others were European isolates, and four Hainan isolates were divided into group Ⅰ. The grouping of STV isolates was related to geographical location, may not be related to the host. The regions with high genomic sequence variability between Hainan isolates and group Ⅰ isolates were 881-1061 nt and 1521-1721 nt, and the regions with high genomic sequence variability between Hainan isolate and group Ⅱ isolate were 2041-2241 nt and 2761-2921 nt. No recombination events were found between STV isolates. This is the first report of STV in Hainan Province. The findings of this study would provide an important basis for understanding the distribution and occurrence trends of STV in Hainan province and for the development of effective surveillance and control measure.