Molecular and histopathological studies were carried out on samples from three Brazilian dogs with persistent hepatozoonosis parasitemia. Canine hepatozoonosis was confirmed by finding gametocytes in blood smears. Histopathological examination of skeletal muscle biopsy revealed muscle degeneration and atrophy, and degenerating/regenerating myofibers, similar to the muscle degeneration caused by Hepatozoon americanum . However, the large cystic structures typical of H. americanum were not observed in muscle biopsies from these dogs. Partial 18S rRNA sequences amplified by PCR from the three Brazilian samples demonstrated closest similarity to the Hepatozoon sp. Fukuoka described in Japan (>99% identity). These results indicate that both additional clinical cases and genes need examination in order to determine the phylogenetic relatedness among canid Hepatozoon species.