The Côte d’Ivoire lethal yellowing (CILY) phytoplasma continues rapidly spreading into new coconut-growing villages, severely affecting the livelihoods of smallholder farmers in Grand-Lahou. Eight villages were surveyed for the CILY phytoplasma presence. Leaves, inflorescences and trunk borings were collected from symptomatic and symptomless coconut trees. Leaves from plant species growing within and in the periphery of the coconut farms were also collected. Total DNA was extracted and tested by nested PCR/RFLP and sequencing with primers targeting the 16S rRNA and the translocation protein (secA) phytoplasma genes. The CILY phytoplasma was detected in 81.2% of the symptomatic trees exhibiting symptoms of the disease stages 2 and 3 from all the villages surveyed, and was shown a trend to move westwards to other coconut-growing areas. CILY phytoplasma was distinguished from the Ghanaian Cape St. Paul Wilt Disease and the Mozambican LY phytoplasmas based on SecA RFLP profiles and SNPs. Plants from five botanical families: Poaceae, Verbenaceae, Plantaginaceae, Phyllanthaceae and Cyperacea were identified as alternative reservoirs for the CILY phytoplasma, which may have epidemiologic implications for the spread of CILY in the coconut farms in Grand-Lahou.