Four sugarcane leaf samples from Cameroon showing mosaic like symptoms tested negative by RT-PCR for potyviruses and a poacevirus causing mosaic in sugarcane. Virus sequences sharing 98–99% nucleotide identity with Sugarcane chlorotic streak virus from Nigeria were found in these four samples by virion-associated nucleic acid metagenomics. Five complete genome sequences were obtained after cloning five isolates from Cameroon. These genome sequences shared less than 75–76% identity with the closest Mastrevirus species, thus confirming that Sugarcane chlorotic streak virus is a new Mastrevirus species. To our knowledge, this is the first report of Sugarcane chlorotic streak virus in Cameroon.