Human babesiosis is a tick-borne infectious disease caused by the multiplication of protozoa of the genus Babesia in erythrocytes. Severe and often fatal human babesiosis in Europe occurs in immunocompromised patients and are mainly due to B. divergens. A 56 year-old man, splenectomised in 2001, came into the emergency room for meningitidis syndrom suspicion on September 2017. Patient suffered fever and headaches for 2 weeks. Then appeared important asthenia, sweats, fast breathing, myalgia, and arthralgia. Babesiosis was diagnosed on blood smear, confirmed by serology and PCR. The patient was successfully treated. As symptoms were atypically mild for a B. divergens infection (usually fulminant and often fatal), we performed a molecular characterisation of the etiological agent based on several conserved (18S rDNA) or variable molecular markers (ama-1 - apical membrane antigen-1 - and rap-1 – rhoptry associated protein-1). We performed the same analysis on B. divergens, as well as on the phylogenetic related deer pathogen B. capreoli and the american zoonotic Babesia sp. MO-1. The 18S rDNA sequence analysis indicated that this parasite differs from B. divergens, B. capreoli and Babesia sp. MO-1, but is more closely related to the american zoonotic Babesia sp. MO-1. The analysis of the other molecular markers (ama-1 and rap-1) on several strains of B. divergens, B. capreoli and Babesia MO-1 demonstrated a low genetic diversity intra-species and a greater diversity between different species. Sequences of the new parasite differed from all of them. The patient was infected by a tick-bite on a french island. This strain has probably evolved separately from the mainland Babesia species. As B. divergens, B. capreoli and Babesia sp. MO-1 have different natural hosts (cattle, roe deer and cottontail rabbits respectively), this new isolate may also have a specific natural host. Its proposition as a new species is debated.