Plasmodium ovale wallikeri and P. ovale curtisi were recently classified as two distinct species. Like P. vivax, both P. ovale curtisi and P. ovale wallikeri have the ability to cause relapse in humans. P. ovale spp. are still understudied and the development of genomic tools to study parasite genetic diversity parameters or medically-important traits such as relapses are needed. Here, we describe a protocol to type a set of eight putatively neutral P. ovale wallikeri microsatellite markers. Expected heterozygosity ranged from 0.764 to 0.940 in 69 P. ovale wallikeri samples from Sub-Saharan Africa and polyclonality was detected in 7 isolates. We genotyped 15 pairs of isolates from primary (D0) and relapsing infections (Drelapse) that occurred in metropolitan France from 2013 to 2021. For most pairs, the D0 and the Drelapse isolates were highly genetically related, an observation that was confirmed by whole-genome sequencing for the four pairs we further studied.