This study aimed to molecularly characterize the Hepatozoon spp. infecting domestic and wild dogs in Brazil. A total of 22 whole blood samples tested positive for Hepatozoon spp., and five samples were sequenced for the 18S rDNA gene from H. canis after PCR amplification with four primer sets. Phylogenetic analysis using Bayesian inference showed that the three H. canis isolates from domestic dogs were not monophyletic; however, they were more closely related to each other than to other H. canis sequences. The isolate from the hoary fox (Lycalopex vetulus) was phylogenetically more distant. Two haplotype networks were constructed, identifying 10 haplotypes of H. canis in Brazil, with H10 constituting the largest group. It contains nine isolates, including three from domestic dogs. The H5 haplotype grouped the sequence of L. vetulus with two additional sequences from hosts Tapirus terrestris and L. vetulus, representing the sole haplotype with wild hosts. Bayesian analysis suggested the possible existence of two genetic groups of H. canis in Brazil, indicating gene flow of this agent within the country. These findings contribute valuable insights for a more comprehensive understanding of the molecular diversity of Hepatozoon spp. in Brazil and may help in the development of effective control measures.