Recent studies have revealed that some intracellular metal ions other than Ca ²⁺ also act as signaling mediators. Detailed analyses of such intracellular metal ion dynamics will enhance our understanding of the physiological roles of these metal ions. Fluorescence imaging is a powerful technique for this purpose owing to its high spatiotemporal resolution. However, with respect to metal ion selectivity, subcellular localization, and robustness to intracellular environmental changes, there are not yet enough fluorescent metal-ion probes suitable for such intracellular analysis. Recently, we have developed several metal ion probes that combine the characteristics of small-molecule fluorescent probes, such as ease of tuning of fluorescence properties and metal ion affinities, with subcellular localizability by a tag protein. In this account, we introduce our recent achievements in the development of small molecule-protein hybrid fluorescent probes and their applications such as long-term imaging of intracellular Mg ²⁺ dynamics and quantification of labile Zn ²⁺ concentration in the Golgi apparatus.