For studying epidemiology and tracking 'Candidatus Phytoplasma palmicola' associated with the coconut lethal yellowing disease in Africa, a Multi Locus Sequence Typing (MLST) scheme was developed and applied to Ghanaian samples collected before 2010 across the country, and samples from the northern provinces of Cabo Delgado and Zambezia in Mozambique (Pilet et al., 2019). To estimate the capacity of the MLSA scheme developed to monitor the evolution in the composition of the pathogen population over time, and to confirm its capacity to detect emerging variants of the pathogen, the scheme was applied to a new set of samples. The sequences of the eight genes constituting the MLSA scheme were obtained for 102 Ghanaian DNA samples collected in 2017, and three Mozambican samples collected in 2018 in the province of Inhambane. In Ghana, two of the six sequence types (STs) identified were new ones. The ST2 is predominant in Central region, ST1 has become main type in the Western Region followed by the new emerging ST9. In Mozambique, the three samples collected in the Province of Inhambane represent three new STs. While apparently genetically linked to the STs from the province of Cabo Delgado and Zambezia, two samples show enough mutations to suggest an ancient introduction, possibly much older than its first observation in 2010 in Vilankulo, province of Inhambane. The third one (ST13) collected in the south of the province (Inharrime district) is very different from all other strains observed so far, suggesting a new and independent introduction of the pathogen. These data would be useful in devising policies on management measures against the disease. This study underlines the power of the MLSA scheme for monitoring 'Ca. P. palmicola'. It is necessary to continue both sampling and characterization of the pathogen in the various affected countries, and to develop similar tool for other diseases associated with phytoplasmas.