Dynamin-1-like protein (Dlp1) belongs to the dynamin superfamily, and is the key enzyme of mitochondrial division. Dlp1 exists as small oligomers that can self-assemble into larger multimeric structures such as rings and tubules. Dlp1 has an N-terminal GTP binding domain, a middle assembly domain, a small insert (B domain), and a C-terminal GTPase effecter domain (GED). In this study, we have solved the crystal structures of a fusion protein of human Dlp1 GTPase domain and a minimal stalk of GED domain in complex with three different nucleotide analogues at 1.7-2.0 Å resolution. The overall molecular structure seen in each nucleotide complex was almost similar to one another. Dlp1 GTPase domain forms a face-to-face dimer, and relative orientation of the stalk sticking out of each GTPase core is trans, while it is cis in the crystal structure of dynamin-1.