<i>Cacao swollen shoot virus </i>(CSSV; genus, <i>Badnavirus</i>; family, <i>Caulimoviridae</i>) has become an increasingly important constraint on cocoa production in West Africa, which supplies about 70% of the world’s cocoa beans. To conduct epidemiological studies, and provide support to breeding and disease management programs, the development of sensitive virus detection and identification methods has become essential. Preliminary studies indicated that CSSV isolates are genetically variable and highly divergent, rendering existing diagnostics ineffective. To test the feasibility of PCR for CSSV detection and differentiation of all isolates and strains in cacao plants, endemic hosts, or the mealybug vectors, PCR primers were designed for six viral genome loci based on seven CSSV genome sequences available in GenBank database. Total DNA extracted from cacao leaves and stems was subjected to rolling circle amplification, followed by PCR. Sequences of cloned amplicons were analyzed to determine the extent of CSSV genomic diversity. Results indicated that isolates from Cote d’Ivoire cacao plant samples were highly variable in certain genomic regions, and conserved in others, and that no one primer pair amplified CSSV in all cases in which it was present. Thus, complete genome sequencing will be required to reveal the full extent of genomic diversity, upon which more accurate diagnostic tools can be based, and implemented to understand the basis for the recent epidemics in West Africa.