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Here we describe the developing of molecular diagnose assays for Cotton blue disease. Previously we sequenced part of the genome of its casual agent Based in alignment analysis of this sequence we designed oligonucleotids pairs that specifically will amplify this virus in infected plants. We tested these pairs of primers in two independent infected plants, a lot coming from Mato Grosso and another lot from Paraná, both of them infected with the same virus isolate. The results obtained showed that the primers were able to amplify virus specific bands in a robust and reproductively manner. Besides the development of this RT-PCR based method we also developed a northern blot assay for this disease using virus CP as probe. Using one or both methods it is now possible to identify precociously Cotton blue disease in fields conditions what may reduce importantly the lost associated with the dissemination of this important disease in Brazilian and others producer countries fields.