Abstract: A study was undertaken to find out the genomic variability in Citrus yellow mosaic virus (CMBV), a bacilliform virus under the genus Badnavirus, infecting different citrus species in India and their phylogenetic relationship with other badnaviruses. Comparison of genome sequences of four isolates of CMBV infecting different species of citrus with previously sequenced three CMBV isolates indicated variability in coding region of ORFs 1, 2 and 3 of all the CMBV isolates infecting same or different citrus species with highest variability in coding region of ORF 3. Coding region of ORF 4, 5, were also highly variable in CMBV isolates but they were highly conserved in CMBV isolates infecting Acid lime. ORF 6 was comparatively conserved and was identical in CMBV isolate infecting Acid lime. All the CMBV isolates shared maximum identity with Cacao swollen shoot virus (CSSV) in ORF 1 and 3 indicating that CMBV isolates are more closely related to CSSV than other badnaviruses. This study has implication in determining the diversity and diagnosis of CMBV.