The discovery of new outbreaks caused by Cacao swollen shoot virus (CSSV) in Côte d'Ivoire in 2003, when this disease seemed to have been eradicated since the end of the 1950s in that country, casts doubt on the sustainability of Ivorian cocoa production. The aims of this study were, first, to carry out a molecular characterization of CSSV isolates from the main outbreaks in Côte d'Ivoire; second, determine their phylogenetic position in relation to isolates already discovered in Togo and Ghana; and, finally, study their geographical distribution to understand the dispersal of the virus. Additionally, this study was intended to enable the implementation and validation of a polyvalent molecular diagnosis assay for CSSV. Sequences analyses, corresponding to a fragment located at the 5′ end of open reading frame (ORF)3 of the CSSV genome, revealed three new CSSV groups (D, E, and F) distinct from the A, B, and C groups already identified in Togo. Only group B was detected in all the outbreaks, whereas groups A and C were not identified in Côte d'Ivoire. In addition, a polymerase chain reaction diagnostic using the ORF3A F/R primer pair was polyvalent, because it enabled the detection of CSSV in 90% of the plots in all the cocoa regions analyzed by this study.