In this report, nanoprobes which could detect the femtogram level of arsenite ions in subcellular organelle of live cells are disclosed. The nanoprobes are composed of ssDNA and single-wall carbon nanotubes (SWCNTs), and the ssDNA is marked by a dye molecule. In a live cell, trace arsenite ions could interact with nanoprobes and significantly decrease the emission of the nanoprobes. With the help of a confocal microscope and cryo-electron microscopy, the lysosome target of the arsenite ion and nanoprobe is well described in high spatial resolution.