Coconut lethal yellowing disease (CLYD) caused by phytoplasma is a destructive disease affecting coconut and other palm species. The disease has been reported in Mozambique, Tanzania, and some West African countries, where millions of coconut trees have been affected. Although the disease was first reported in 1999 in Northern Coast of Kenya, no further studies have been conducted, leaving the giant coconut industry at risk of destruction. It is for this reason that a surveillance was undertaken to study the extent of the disease spread and the specific Candidatus phytoplasma strain causing the disease. A total of 125 coconut tree samples were collected in Kwale, Kilifi, Lamu, and Tana River counties by drilling the tree trunks aseptically. DNA extractions were done, followed by PCR process done using P1/P7 universal primers, gel electrophoresis and amplicon sequencing. For the coconut tree drillings results, the BLAST comparison with existing data in the NCBI database revealed it to be Candidatus phytoplasma palmae strain isolate Tanz08, under gene accession No. GU952107.1. Further phylogenetic analysis using the maximum likelihood method indicated that the strain is closely related to those reported in Tanzania. The CLYD positive samples were identified from Lamu and Kwale counties, with 6 cases from each County. Although there were no positive cases reported in Kilifi and Tana River counties, the presence of the vectors suggests that more studies need to be done on the disease. Further studies should be done on the alternative hosts, varieties prone to the disease, characterization and diversity of the vectors, the incubation period and the host pathogen relationship.