In May 2013, typical symptoms of bacterial spot disease were observed on tomato. Symptoms were characterized by dark, circular to irregular spots on leaves, and water-soaked spots surrounded by chlorotic halos on fruits. The disease incidence on tomato varied from 48 to 60% in different commercial fields. Diseased fruits and mature leaves were collected from 9 commercial processing fields in Cameron Highlands (Pahang, Malaysia). Based on biochemical, morphological, molecular (nucleotide sequence and phylogenetic analysis) and pathogenicity tests, the causal agent was identified as X. gardneri. This is thought to be the first report of bacterial spot of tomato caused by X. gardneri in Malaysia.