MELK is a cell cycle-regulated protein kinase involved in cell cycle progression, proliferation, tumor growth and mRNA splicing. MELK is localized in the cytoplasm and the nucleus during interphase and at the cell cortex during anaphase and telophase. In this report, we show that the regulatory domain of Xenopus MELK when tagged at its C-terminus with the green fluorescent protein (GFP), co-localizes with mitochondria in Xenopus XL2 cells. Significantly, the presence of a mitochondrial targeting signal at the N-terminus of this fusion protein was predicted by bioinformatics analyses. In agreement with previous reports on mitochondrial proteins, placing the GFP at the N-terminus inhibited the mitochondrial targeting of the MELK fragment and, furthermore, the regulatory domain without a tag co-localizes with mitochondria. These results demonstrate the presence of a mitochondrial targeting signal at the N-terminus of the MC domain of MELK. This mitochondrial targeting signal was also functional in human HeLa cells.