We have observed substantial changes in the resonance Raman spectrum of ruthenium red when it is added to calcium ion binding molecules and organelles, including proteins, phospholipids, chelating agents, and intact mitochondria. The addition of Ca2+ ions can reverse these observed spectral changes. In the case of cytochrome c, ruthenium red binding varies with oxidation state in a manner parallel to that for Ca2+ binding. The resonance Raman spectrum of a ruthenium red-phospholipid complex shows differences from that of a ruthenium red-protein complex, enabling us to distinguish between binding to these different classes of molecules. Our studies suggest that the primary constituent of the low-affinity Ca2+ binding sites in mitochondria is cardiolipin.