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Background   Hepatozoon canis  is a protozoan transmitted to dogs and other wild carnivores by the ingestion of ticks containing mature oocysts and is considered the principal cause of canine hepatozoonosis in the world. Here, we examined ribosomal RNA 18S gene sequence variation to determine the genetic differences and phylogeographic diversity of  H. canis  from various geographical areas around the world.    Methods  We used 550 publicly available sequences of  H. canis  from 46 countries to assess haplotype relationships, geographical structure, genetic diversity indices, and relationships among populations. We performed neutrality tests and pairwise comparisons of fixation index ( F  ST ) values between groups and pairwise comparisons of  F  ST  values between populations. To determine whether populations are structured, analyses of molecular variance (AMOVAs) and spatial analysis of molecular variance (SAMOVA) were performed.    Results  The dataset of  H. canis  yielded 76 haplotypes. Differentiation among populations indicated that there is no phylogeographical structure ( G  ST  = 0.302 ± 0.0475). Moreover, when samples were grouped by continents a significant  F  ST  was obtained, meaning that populations were genetically differentiated. The AMOVA showed that 57.4% of the genetic variation was explained by differences within populations when all locations were treated as a single group and revealed that there is no population structure when populations are grouped into two, three, and four groups ( F  CT ,  p  > 0.05), suggesting that dispersal between populations is high. SAMOVA revealed significant  F  CT  values for groups  K  = 5. The Tajima’s  D  and Fu’s  Fs  show that populations have undergone recent expansion, and the mismatch distribution analysis showed population expansion (multimodal distribution).    Conclusions  The current molecular data confirmed that  H. canis  does not show phylogeographic or population structure. The haplotypes exhibit low genetic differentiation, suggesting a recent expansion due to gene flow among populations. These results provide pivotal information required for future detailed population genetic analysis or to establish control strategies of this parasite.    Graphical abstractSupplementary Information  The online version contains supplementary material available at 10.1186/s13071-021-04924-x.

Phylogeography and population differentiation in Hepatozoon canis (Apicomplexa: Hepatozoidae) reveal expansion and gene flow in world populations