AbstractCape St. Paul Wilt Disease (CSPWD), the Ghanaian form of the lethal yellowing‐type diseases associated with phytoplasmas, is yet the major factor affecting the coconut industry in Ghana since 1932. Recently, a PCR assay based on a non‐ribosomal gene sequence was developed for the detection of the CSPWD phytoplasma in the West Region. Our study aimed at comparing the performance of the non‐ribosomal PCR to existing ribosomal PCRs and determine the best assay to use for the detection of the CSPWD phytoplasma within the three major coconut‐growing regions: Central, Western and Volta and in palms at different ages and disease stages. To determine the most affected region, 163 CSPWD‐affected coconut palms from 32 locations from the Central, Western and Volta Regions were randomly sampled. The analysis of the presence of the CSPWD phytoplasma in coconut palms of different ages showed that palms within the age brackets (1–10), (11–20) and (61–70) years were the most affected by CSPWD. The disease was most widespread in the Central, followed by the Western, then the Volta Region. A Euclidean similarity analysis of the infection rate across palm ages revealed three distinct clusters at a linkage distance of 6.5. The PCR assay based on the secA gene sequence yielded the highest number of coconut palms positive for the CSPWD phytoplasma compared to PCR assays targeting phytoplasma ribosomal genes. These results report an update on the detection of the CSPWD phytoplasma in the CSPWD‐affected coconut regions and across coconut palms representing different ages and disease stages and provide valuable information to support the CSPWD management in Ghana.