Mitochondria are dynamic organelles that undergo fusion, fission, and translocation. The dynamic property is essential for establishing energy-consuming biological processes including cellular differentiation. Early ultrastructural studies have shown that mitochondria of mammalian spermatogenic cells dramatically change their number, size, distribution, and internal structure. However, its regulatory mechanism is largely unknown. In course of searching for molecules involved in the mitochondrial morphogenesis in spermatogenesis, we identified mouse gametogenetin-binding protein 1 (GGNBP1), a DUF1055 domain-containing protein of unknown function, as a mitochondrial protein. When GGNBP1 was expressed in COS7 cells, it was localized in the intermembrane space and induced an extensive fragmentation of mitochondria in the manner dependent on the activity of the mitochondrial fission factor DNM1L. Deletion mutant analyses demonstrated that the N-terminal region is required for its mitochondrial targeting and that the C-terminal region including the DUF1055 domain is responsible for the mitochondrial fragmentation activity. Immunohistochemistry of mouse testis revealed that GGNBP1 is highly expressed in the late pachytene spermatocytes and early round spermatids. However, a subcellular fractionation study showed that it is localized to not only mitochondria but also other membranous compartments in vivo. These results suggest that GGNBP1 is involved in spermatogenesis by modifying mitochondrial dynamics and morphology.