Background: A Lethal Decline associated with a phytoplasma has been observed in different localities of the western coast of Madagascar on coconut trees. Classical investigations based on 16Sr rRNA gene sequences suggest a very close genetic proximity (Identity 99%) with the phytoplasma associated with the Coconut Lethal Decline in Tanzania responsible for the loss of millions of coconut trees in East Africa. To further understand their relatedness, we used a genome-driven approach. Methods: One strain originated from Tanzania and one from Madagascar were sequenced by Illumina, combinated with Nanopore technology for the Malagassy strain, draft genomes were assembled and percentage of Average Nucleotide Identity (ANI) was calculated. Identity for concatanated sequences of the eight genes constitutive of the MLST scheme previously developed for `Ca. Phytoplasma palmicola` was also calculated. Results: A single contig of 505 kb was assembled for the Malagassy strain while a fragmented genome of 398 kb was obtained for the Tanzanian strain. An ANI of 88% was calculated between strains from the two origins. A percentage of identity of 91.2 was calculated for the concatenated housekeeping genes sequences. Conclusion: Similar to many culturable bacterial genera, ANI and MLSA could refine the accurate delimitation of `Candidatus phytoplasma` species still currently defined using 16Sr RNA gene identity. Herein and in disagreement with 16Sr, both ANI and MLSA suggest that Malagassy strain represent a new `species` (ANI95% with Coconut Lethal Decline in Tanzania).