In East Africa, Lethal Yellowing-Type Syndromes have profoundly and lastingly affected the coconut industry. While 'Candidatus Phytoplasma palmicola' has decimated industrial plantations in Mozambique, 'Candidatus Phytoplasma cocostanzania' is affecting coconut groves in neighboring Tanzania and in Kenya. A first multilocus sequence typing (MLST) scheme based on eight housekeeping genes was developed to study 'Ca. Phytoplasma palmicola'. Here we present a new but similar MLST scheme developed to sustain epidemiological studies on 'Ca. Phytoplasma cocostanzania' and later comparison of the two phytoplasmas. Primer pairs were defined to amplify identical portions of the 8 genes (gyrB, leuS, lpd, recA, rplV, rsmI, and secA) and applied to 25 DNAs from Lethal Decline symptomatic coconut trees originated from Tanzania. The eight gene sequences were concatenated for each sample producing a sequence of 4383 nucleotides. The average %GC of the concatenated sequences is low as 25.5. Data analysis reveals 16 different haplotypes among the 25 samples (Hd: 0.960), and a nucleotide diversity (pi) of 0.00354, increasing drastically the discrimination of the strains. The most variable genes are lpd and secA each with seven sequence types (ST). Our tool provides sufficient resolution for effectively analyzing 'Ca. Phytoplasma cocostanzania' diversity at the regional level, and for allowing the epidemiological monitoring of lethal decline disease.