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Guggal (Commiphora wightii (Arnott) Bhandari comb. nov.) is a small tree which is tapped for medicinally important oleo-gum-resin. Naturally infected plant oozes oleo-gum-resin from its trunk and primary branches. However, in either case, the plant dies slowly after oozing. A bacterium was established to be responsible for these phenomena. Four isolates of this bacterium were characterised by biochemical tests, Biolog GN2 microplate reaction, rDNA sequencing, which suggested that the pathogen belonged to the genus Xanthomonas. However, phylogenetic analysis based on chaperone protein (dnaK) gene, TonB-dependent receptor (fyuA) gene, DNA gyrase B (gyrB) gene and RNA polymerase sigma factor (rpoD) gene sequences placed it as a member of X. axonopodis 9.2 rep-PCR/DNA-DNA homology cluster close to X. perforans, X. alfalfae and X. euvesicatoria. Further elucidation of phylogenetic position of the test strains was achieved from a gyrB based tree considering sequences from 71 representative strains. Test strains were confirmed to be members of X. axonopodis. These had very narrow infectivity limited to Commiphora spp. Hence, we propose a novel pathovar, X. axonopodis pv. commiphoreae pv. nov. as the cause of gum oozing in guggal. Pathotype is DXA 01 = CFBP 7580 = LMG 26789.