Heartwater, caused by the intracellular bacterium Ehrlichia ruminantium, is a major tick-borne disease of livestock in Africa also introduced in the Caribbean. The main problem encountered with the control of this disease is the lack of efficient vaccine in the field. This is thought to be related to the high genetic diversity of strains circulating in a same area. A set of eight circulating strains was isolated from a herd of cows in a small locality in Burkina-Faso and analyzed along with two reference strains, i.e. ERGA and ERWO, for which full-length genome was available. A MLST analysis was developed based on the genes gltA, groEL, lepA, lipA, lipB, secY, sodB and sucA. Phylogeny analysis was conducted both on concatenated MLST loci and on each individual locus. This showed differing phylogenies for each individual target gene. Most of the recorded polymorphism was borne by three strains: 331, 469 and 623. The neutrality hypothesis could not be rejected. Recombination and linkage disequilibrium were shown to have occurred. A core of seven strains displayed little polymorphism and signs of most likely ancient recombination events. The two reference strains, one from the Caribbean separated from west African strains three centuries ago and another one isolated in South Africa, were very closely related to the core strains whereas the three differing strains displayed recombination and most of the parcimony informative sites. These data suggest that some strains are in genomic stasis, as expected for intracellular parasites, while others emerge in the same area with DNA polymorphism. This work also shows that the MLST scheme developed can discriminate between these two kinds of strains.