In November 2013, symptoms of yellowing on leaves and brown necrotic rot on tuberous roots were observed on different cassava landraces (Manihot esculenta) in Dembeni on Mayotte Island, a French Overseas Department in the south-west Indian Ocean. The symptoms, similar to the cassava brown streak disease described in East Africa, suggested the possible involvement of cassava brown streak viruses (Mbanzibwa et al., JGV 2011). The expanding cassava brown streak disease epidemic in East Africa is caused by two ipomoviruses, Cassava brown streak virus (CBSV; Monger et al., Arch. Virol.2010) and Ugandan cassava brown streak virus(UCBSV; Winter et al., JGV 2010). To verify the identity of the causal agent, symptom-bearing leaf samples of 17 affected plants were collected in March and June 2014.For the detection of cassava brown streak viruses, a two-step RT-PCR using CBSDDF2 and CBSDDR primers was used (Mbanzibwa et al., JGV 2011). These primers were designed for simultaneous virus-specific detection of CBSV and UCBSV (amplicons of 344 bp and 440 bp, respectively). RT-PCR products of the expected size for UCBSV were obtained for 11 samples. To confirm the diagnosis, the RT-PCR products were directly and bi-directionally sequenced and contigs assembled. Sequences of 376 bp from eight of the 11 samples were obtained which had 99-100% nucleotide identity (EMBL Aaccession Nos. LN611671 to LN611678). The sequences showed the highest nucleotide identity (86%) with isolates of UCBSV from Uganda and Malawi (FN434109; FN433932) and 85% with an isolate of CBSV from Mozambique (FN434436). A phylogenetic reconstruction with publicly available complete genome sequences of cassava brown streak viruses confirmed that the Mayotte isolates are genetically more related to UCBSV isolates than to CBSV isolates from East Africa, and represent a separate lineage that appears to be almost intermediate between current isolates of CBSV and UCBSV. This is the first report of cassava brown streak di