The Sugarcane Yellow Leaf disease is a major viral disease of sugarcane, caused by a Polerovirus - the SCYLV- transmitted by several aphid species. The disease was described only in the 1990s probably because yellowing of the leaves, the main symptom, may be confused with abiotic stress. Yellow leaf disease is widely distributed in sugarcane growing areas where yield losses have been reported. Varietal resistance, both against the virus and its vectors, is the most practicable control method and a recent objective in breeding programs. In order to analyze the genetic basis of the resistance to SCYLV and to its worldwide aphid vector Melanaphis sacchari, we undertook an association mapping study based on 344 sugarcane cultivars. These 344 cultivars were split in two populations sharing 29 common cultivars, and evaluated in two contrasted environments, one in Réunion Island in the Indian Ocean (RUN, 184 cultivars) and one in Guadeloupe in the Caribbean (GUA, 189 cultivars). The RUN (one trial) and the GUA (two trials) populations were evaluated in the field in second ratoon under natural infestation conditions for SCYLV incidence by tissue-blot immunoassay. BRA-PER, CUB and RUN genotypes of the SCYLV were recorded by PCR in the GUA population. SCYLV genotypes detected in the RUN population were BRA-PER and RUN the latter representing the majority of the samples. The Réunion population was also evaluated for M. sacchari infestation level during two cropping seasons. Both populations were genotyped with AFLP markers (1367 markers for RUN and 2421 markers for GUA) and DArT markers (1877 markers for RUN and 1560 markers for GUA). Genetic structure of both populations was analyzed by a Principal Component Analysis (PCA) approach with the EIGENSOFT software, using 2092 independent markers for RUN and 2576 independent markers for GUA. Significant marker - trait associations were detected with the TASSEL software, using a mixed linear model taking into account structure and f