100 horse in Switzerland were tested for piroplasms by reverse line blotting.
2 horses were positive for T. equi, 5 only with the Theileria genus-specific probe.
Sequencing of the 18S rRNA gene suggested the presence of novel T. equi variants.
The results showed there were two variants or genotype of T. equi in Swiss horses.
Our data are crucial to improve molecular diagnostic tools and increase awareness.