Recent genetic diversity studies suggested the existence of several genotypes of Sugarcane yellow leaf virus (SCYLV), the causal agent of yellow leaf of sugarcane. In order to identify and more precisely describe the genotypes of SCYLV, we sequenced the entire genome (six ORFs) of eight virus isolates from six geographical locations (Brazil, China, Colombia, Cuba, Peru, and Reunion). Four genotypes of SCYLV (BRA for Brazil, CUB for Cuba, PER for Peru and REU for Reunion) were identified based on phylogenetic analyses with the genome sequence of these eight isolates. Specific primer pairs were designed to identify the SCYLV genotypes by RT-PCR. A unique genome fragment was amplified from each genotype, with the exception of genotypes BRA and PER which are relatively close. The RTPCR primers were then used to identify genotypes of SCYLV present in three different sugarcane growing locations: Colombia, Guadeloupe and Reunion. Out of 41 sugarcane leaf samples from Colombia, 15 were infected by genotype BRA/PER, 19 by genotype CUB and 7 by genotypes BRA/PER and CUB. Both genotypes were found in locally bred CC varieties and in foreign varieties, but incidence of genotype CUB (84%) was higher than incidence of genotype BRA/PER (44%) in the 10 CC varieties. Out of 64 samples from Guadeloupe, 12 were infected by genotype BRA/PER, 13 by genotype CUB, 37 by genotype REU and 2 by genotypes CUB and REU. The three genotypes were found in locally bred FR varieties and in foreign varieties. In the 15 FR varieties, incidence of genotypes BRA/PER, CUB and REU was 16%, 37% and 47%, respectively. Out of 51 samples from Reunion, 2 were infected by genotype BRA/PER, 29 by genotype REU and 20 by genotypes BRA/PER and REU. Only genotype REU was found in the 29 samples from the 4 locally bred R varieties. All samples infected by genotypes BRA/PER and REU (or only BRA/PER) were obtained from variety SP71-6163. Several genotypes of SCYLV can therefore co-exist in a geographical location or w