We report a two-photon probe (SZn-Mito) for mitochondrial zinc ions ([Zn2+]m). This probe shows a 7-fold enhancement of two-photon-excited fluorescence in response to Zn2+ with a dissociation constant (KdTP) of 3.1 卤 0.1 nM and pH insensitivity in the biologically relevant range, allowing the detection of [Zn2+]m in a rat hippocampal slice at a depth of 100鈭?00 渭m without interference from other metal ions through the use of two-photon microscopy.