Abstract: 【Objective】 This study aimed to identify the viral pathogens causing leaf curl and plant stunting in Guangxi cigar tobacco and flue-cured tobacco， and to perform genetic evolution and recombination analyses on their isolates to clarify the pathogen and its genome sequence characteristics， thereby providing a theoretical basis for integrated prevention and control of tobacco viral diseases. 【Method】 Samples of cigar tobacco and flue-cured tobacco with symptoms suspected of being caused by geminiviruses， such as plant stunting， leaf crinkling， and leaf curl， were collected from tobacco fields in Jingxi， Guangxi. Molecular identification and recombination analysis were performed using PCR detection， gene cloning， sequence determination， recombination analysis， and phylogenetic tree construction. 【Result】 According to amplification results of degenerate primers （PA/PB） of geminiviruses， target segments of approximately 500 bp were obtained from both cigar tobacco and flue-cured tobacco samples. PCR products were purified and sequenced， and the obtained sequences shared a nucleotide similarity of over 91.00% with pepper leaf curl Yunnan virus （PepLCYNV） registered in GenBank， confirming that the tobacco samples were infected by the virus of Begomoviruses. No bands were amplified using universal primers for β satellites（β01/β02）， indicating the absence of β satellites in the samples. Two pairs of back-to-back primers were designed to amplify the DNA-A of the two samples. Sequencing and assembly yielded a complete genome sequence of approximately 2756 bp from the infected cigar tobacco， designated as PepLCYNV-GX-XJ， and a complete genome sequence of approximately 2758 bp from the infected flue-cured tobacco， designated as PepLCYNV-GX-YY. Nucleotide sequence alignment showed that the complete genome sequences of PepLCYNV-GX-XJ and PepLCYNV-GX-YY shared a similarity of 95.50%； both isolates exhibited high nucleotide similarity with previously reported PepLCYNV isolates registered in GenBank， with the highest similarity（91.74%）with PepLCYNV-YN2023. Recombination analysis revealed that both PepLCYNV-GX-XJ and PepLCYNV-GX-YY were recombinant viruses， with 2 recombination events detected in the regions spanning nucleotides of 2734-1467 and 2567-2701 nt. Phylogenetic analysis showed that PepLCYNV-GX-XJ and PepLCYNV-GX-YY clustered together in 1 branch， while the other 11 PepLCYNV isolates clustered in a separate branch， implying that PepLCYNV-GX-XJ and PepLCYNV-GX-YY shared the closest relationship， probably sharing the same evolutionary origin. 【Conclusion】 The symptoms of plant stunting， leaf crinkling， and leaf curling in cigar tobacco and flue-cured tobacco are caused by a virus of Begomovirus and Geminiviridae， and the viral pathogen is PepLCYNV.