We introduce here a new class of BODIPY-based Ca2+ indicators which can be derivatized with biological ligands that permit the localization of the indicators in living cells. The underivatized BODIPY-based Ca2+ indicator (BOCA-1) shows a 250-fold increase in fluorescence intensity upon Ca2+ binding. We also prepared its O6-benzylguanine (BG) derivative, BOCA-1-BG, which can be covalently and specifically linked to SNAP-tag fusion proteins in living cells. The indicator retains its properties as a highly sensitive Ca2+ indicator after conjugation to proteins, displaying a 180-fold increase in fluorescence intensity upon Ca2+ binding. We further demonstrated that BOCA-1-BG through reaction with localized SNAP-tag fusion proteins can be used to sense changes in Ca2+ concentrations in the nuclei and in the cytosol of live CHO-K1 cells. The high sensitivity of the indicator together with the possibility to selectively couple it to proteins of interest makes it a powerful tool for measuring local changes in Ca2+ concentrations in living cells.