Members of the genus Hepatozoon (Miller, 1908) are blood parasites found in a wide range of host species, including wild rodents; however, information about the life cycle, distribution and Hepatozoon species diversity infecting these mammals are lacking. We studied the parasite stages and DNA sequences of Hepatozoon sp. of 11 naturally infected Akodon montensis. Thin blood smears, tissue samples and whole blood were obtained for morphology, morphometry and molecular analyses. Seven of the 11 rodents had gamonts on the blood smears. Biological and morphological features of the parasite such as tissue tropism, gamonts and meronts size and morphology, as well as the DNA sequence comparison and phylogenetic analysis, indicated that the Hepatozoon sp. detected in this study is distinct from those species previously reported in small rodents. Herein, we propose a new species, named Hepatozoon milleri sp. nov. This is the first description of a new Hepatozoon species from wild small rodents in Brazil, based on morphological and molecular characteristics.