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Effective plant disease management requires quick, accurate and specific diagnostic techniques, which in turn help in disease surveillance, regulation of material movement and ensure good quality planting material. When investigating emerging diseases with no existing specific diagnostic protocols, it can be useful to apply tools detecting all members of a genus as one. On the other hand, the banana xanthomonas wilt devastating East and Central Africa had no specific detection tool available over ten years after its first report. In this article, we present molecular diagnostic tools developed for genus, species and pathovar specific detection of Xanthomonas campestris pv. musacearum (Xcm). The tools included; i) primers developed based on the internal transcribed spacer region (ITS) of the ribosomal DNA (X-ITS) and a xanthan biosynthetic gene (gumD) (X-gumD) for genus level Xanthomonas detection; ii) primers based on the hypothetical protein NZ_ACHT01000085 (NZ085) for specific detection of the species X. vasicola and the general secretion protein D NZ_ACHT01000280 (GspDm) for specific detection of Xcm. The X- ITS and X-gumD primers specifically amplified DNA from xanthomonads giving 254 and 402 bp fragments, respectively without amplifying DNA of non-xanthomonads. PCR primers NZ085 specifically amplified a 349 bp fragment from DNA of Xcm, X. vasicola pv. holcicola (Xvh) and X. axonopodis pv. vasculorum (Xav) proposed to belong to the species X. vasicola. The GspDm primers amplified a 265bp DNA fragment of Xcm isolates tested with no DNA amplification of other plant associated-bacteria, including the two closely related Xvh and Xav. This provides a promising disease detection approach for both unknown and suspected pathogens.