Several strains of Cocoa swollen shoot virus (CSSV) cause cocoa swollen shoot disease (CSSD) in cocoa (Theobroma cacao L) in Ghana and West Africa. The objectives of this study were to establish the genetic diversity and spatial distribution of the CSSV in Ghana, investigate the epidemiology of CSSD, and the origin and spread of CSSV in Ghana and West Africa. A total of 3-5 leaves per tree, were sampled from infected cocoa and alternate host plants from all the cocoa growing regions in Ghana and also from the CSSV museum of the Cocoa Research Institute of Ghana between January, 2013 and December, 2015. PCR amplifications, cloning and sequencing, phylogenetic relationship analyses and epidemiological analyses were carried out on the DNA extracted from these samples. Phylogenetic relationship analyses revealed the existence of nine CSSV groups A, B, C, E, G, J, K, L and M with six groups detected for the first time in Ghana. The CSSV groups in Ghana were very divergent and corresponded to at least four different putative species (A, B-C complex, E-G-J-K-L complex and M) with the M species detected only on alternate host plants. The spatial distribution of the different molecular groups of CSSV in Ghana makes it difficult to predict a single origin for CSSV amongst the cocoa growing regions in Ghana. Therefore, it could be assumed that the different putative CSSV species emerged from different sources at different times. Moreover, the notion that CSSV originated from alternate host plants could be valid since the M species of CSSV has not yet been detected on cocoa trees.