In Ghana, coconut lethal yellowing phytoplasma locally called Cape Saint Paul Wilt Disease (CSPWD) is the most damaging coconut disease. Two different foci of the disease can be distinguished: the first one covering the coast of the Western and Central Regions, and the second covering the coast of the Volta region. To test the hypothesis of a genetic differentiation between the CSPWD phytoplasma from the two foci, the partial ribosomal operon 16S, and two ribosomal protein genes (rplV and rpsC) of 14 strains were sequenced. The ribosomal protein gene sequences allowed the differentiation of the strains originating from the two different foci by a unique SNP, confirming a genetic differentiation.