Sorghum mosaic virus (SrMV) and Sugarcane mosaic virus (SCMV) cause mosaic disease (MD) in sugarcane; however, SrMV has been the primary cause of MD in Louisiana sugarcane for over 70 years. Prior to the 2000s, strains of SCMV and SrMV were identified by symptoms expressed in a set of host plant differentials. Since 2002 a reverse transcriptase-polymerase chain reaction (RT-PCR) protocol has been used to distinguish between SCMV and SrMV and a restriction fragment length polymorphism (RFLP) analysis of the RT-PCR product to identify the strains of the SCMV or SrMV characterized by host differentials. However, the RFLP banding patterns of an increasing number of SrMV isolates collected annually in Louisiana do not match the patterns of recognized strains of SrMV. Phylogenetic analysis was performed using the RT-PCR sequences from 54 SrMV isolates collected between 2012 and 2018 from 31 released and near-release sugarcane cultivars. Those with similar RFLP banding patterns were grouped together. Five groups were identified and a phylogenetic analysis revealed similar genetic diversity among the SrMV isolates from Louisiana. An inoculated field experiment has been established to determine pathogenicity of isolates representing the genetic diversity among the SrMV isolates across sugarcane cultivars with different levels of mosaic resistance.