Babesiaspp. are intraerythrocytic apicomplexans that digest and utilize red blood cells in a similar way to intraerythrocyticPlasmodiumspp., but unlike the latter, are not sensitive to artemisinin. A comparison ofBabesiaandPlasmodiumgenomes revealed thatBabesiagenomes, which are smaller than those ofPlasmodium, lack numerous genes, and especially haem synthesis-related genes, that are found in the latter. Single-cell sequencing analysis showed that the different treatment groups ofBabesia microtiwith expressed pentose phosphate pathway-related, DNA replication-related, antioxidation-related, glycolysis-related, and glutathione-related genes were not as sensitive to artemether asPlasmodium yoelii17XNL. In particular, pentose phosphate pathway-related, DNA replication-related, and glutathione-related genes, which were actively expressed inP. yoelii17XNL, were not actively expressed inB. microti. Supplying iron in vivo can promote the reproduction ofB. microti. These results suggest thatBabesiaspp. lack a similar mechanism to that of malaria parasites through which the haem or iron in hemoglobin is utilized, and that this likely leads to their insensitivity to artemisinin.Graphical AbstractSupplementary InformationThe online version contains supplementary material available at 10.1186/s13071-023-05783-4.