To sustain epidemiological studies on coconut lethal yellowing disease (CLYD), a devastating disease in Africa caused by a phytoplasma, we developed a multilocus sequence typing (MLST) scheme for 'Candidatus Phytoplasma palmicola' based on 8 housekeeping genes. At the continental level, eight different sequence types were identified among 132 'Ca. Phytoplasma palmicola-' infected coconuts collected in Ghana, Nigeria and Mozambique where CLYD epidemics are still very active. 'Ca. Phytoplasma palmicola' appeared to be a bacterium submitted to strong bottlenecks, reducing the fixation of positively selected beneficial mutations into the bacterial population. This phenomenon, as well as a limited plant host range, could explain the observed country-specific distribution of the eight haplotypes. As an alternative means to increase fitness, bacteria can also undergo genetic exchange; however, no evidence for such recombination events were found for 'Ca. Phytoplasma palmicola'. The implications for CLYD epidemiology and prophylactic control are discussed. The usefulness of seven housekeeping genes to investigate the genetic diversity in the genus 'Candidatus Phytoplasma' is underlined. IMPORTANCE: Coconut is an important crop for both industry and small stakeholders in many intertropical countries. Phytoplasma-associated lethal yellowing-like diseases have become one of the major pests that limit coconut cultivation as they have emerged in different parts of the world. We developed a multilocus sequence typing scheme for tracking epidemics of 'Ca. Phytoplasma palmicola', which is responsible for coconut lethal yellowing disease (CLYD) on the African continent. MLST analysis applied to diseased coconut samples collected in western and eastern African countries also showed the existence of three distinct populations of 'Ca. Phytoplasma palmicola' with low intrapopulation diversity. The reasons for the observed genetic bottlenecks resulting in strong geographic patterns remai