After entering a cell, most small molecule fluorescent probes are dispersed in the cytoplasm before they then accumulate in a specific organelle or subcellular zone. Molecules that can enter two or more organelles with high selectivity are all but unknown. In this work, we report a naphthalimide-based fluorescent probe, NIM-7, that allows lipid droplets and lysosomes to be labelled simultaneously and with high specificity. These subcellular entities can then be visualized readily through yellow and red fluorescence, using different excitation and detection channels. NIM-7 allows 3D imaging and quantitative visualizing of lipid droplets and lysosomes. It is also able to track simultaneously the movement of lipid droplets and lysosomes in real-time. We also report here that NIM-7 can be used to image both different cell lines and zebrafish embryos.