Lemon is valued for its nutritional and therapeutic benefits. Its production in the northern region of West Bengal is severely affected by citrus canker, one of the most destructive bacterial diseases of citrus. The isolation of different bacterial isolates for the present investigation was performed during 2024. Whereas the virulence study was conducted across two cropping seasons (2024–25) to identify the virulent bacterial isolates associated with citrus canker under the local conditions of North Bengal. Twenty bacterial isolates were obtained and they were evaluated through pathogenicity test. Among the isolates, five showed consistent virulence under artificial inoculation conditions. Isolate no. 4 (UBKVXAC4) was found to be most virulent, showing maximum disease severity index (39.43 % in first year and 40.05 % in second year) and disease increase percentage (64.57 % and 67.79 % in first and second year). Molecular characterisation using 16S rRNA gene sequencing identified three isolates as Xanthomonas axonopodis pv. citri, while two were identified as Pantoea agglomerans, suggesting a potential involvement in the development of canker-like symptoms. Further confirmation using Xac-specific primers targeting the hrpW gene showed amplification only in X. axonopodis pv. citri isolates, whereas no amplification was detected in the P. agglomerans isolates. The findings indicate that, besides the primary citrus canker pathogen, P. agglomerans may also be associated with canker-like symptoms in lemon under the agro-climatic conditions of northern West Bengal. This study highlights the diversity of bacterial communities associated with citrus canker and provides useful information for future disease management and resistance screening programmes.