The Cotton Blue disease is an important pathology that affects cotton crops in Brazilian savanna, causing important economical losses, mainly due to preference of the producers in the utilization of susceptible cotton cultivars. This disease is transmited by the Aphis gossipy in a persistent circulative manner. Symptoms and aphid-restricted transmission have prompted researchers to speculate that Cotton blue disease could be attributed to a member of the Luteoviridae family. However, there were no molecular evidences supporting this hypothesis. In a recent work, we amplified and sequenced 1405 nt corresponding to part of the RNA dependent RNA polimerase protein (RdRp), the full intergenic region and the capsid sequence, of a new virus in cotton plants showing disease symptoms collected in Mato Grosso state. Sequence analyses classify this virus as a member of the Polerovirs genus (Luteoviridae family). For the identified virus, we propose the putative name of Cotton leafroll dwarf virus (CLRDV). In this work we analized the genetic diversity of the capsid sequence from CLRDV and used specific primers to amplify this sequence from plants showing disease symptoms collected in three brazilian states: Mato Grosso, São Paulo and Goiás. In addition, degenerated primers that amplify part of RdRp and full intergenic region were used to check the existence of others Polerovirus associated with the disease in plants from Mato Grosso. Sequence analyses confirmed the presence of CLRDV in every infected plant sample and revealed high similarity between the isolates. Comparison of the CLRDV capsid amplified sequences to the CP of CLRDV from Mato Grosso original isolate showed that the virus populations are highly conserved and similar. We didn’t find any other Polerovirus assocated with Cotton blue disease in the samples analized. The current data initiate the map of CLRDV infection in Brazil, moreover to have used, for the first time, the test of molecular diagnosis confirming its efficiency.