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In this study, we developed organelle-specific blue-emitting two-photon (TP) probes for Ca2+ (BCa-1 , BCa-2 mito , and BCa-3 mem), with absorption maxima (λ max) at 350–358 nm, emission maxima (λ fl) at 464–466 nm, and TP action cross-section (Φδ max) values of 55–70 × 10−50 cm4s/photon, in the presence of excess Ca2+ at 750 nm. Moreover, the probes had dissociation constants of 0.18, 2.7, and 100 μM, respectively, which are appropriate values for sensing Ca2+ in the cytoplasm, mitochondria, and plasma membrane, respectively. The measurements were conducted using a calcium calibration buffer (10 mM 3-[ N -morpholino]propanesulfonic acid and 100 mM KCl) at pH 7.2. The TP microscopy results revealed that the probes could facilitate the real-time detection of Ca2+ in the cytoplasm, mitochondria, and plasma membranes of live cells and tissues. Additionally, we developed a green-emitting TP probe for H+ (FHEt-1 lyso) with λ max = 359 nm, λ fl = 571 nm, and Φδ max = 70 × 10−50 cm4s/photon at pH 4.3 in a universal buffer (0.1 M citric acid, 0.1 M KH 2 PO 4 , 0.1 M Na 2 B 4 O 7 , 0.1 M tris[hydroxymethyl]aminomethane, and 0.1 M KCl); this probe could detect H+ in the lysosomes. Using BCa-1 and FHEt-1 lyso , it was possible to simultaneously monitor the changes in cytosolic Ca2+ and lysosomal H+ concentrations in live cells and tissues using dual-color TP microscopy in real time. When used with TP probes emitting wavelengths of green light or longer, these blue-emitting Ca2+ probes can be used to investigate the physiological role of Ca2+ in cellular organelles as well as the crosstalk between Ca2+ and other metal ions in specific organelles. [Display omitted] • We developed organelle-specific blue-emitting two-photon Ca2+ probes. • They can detect Ca2+ in organelles of living cells and tissues in real-time. • They have appropriate K d values for Ca2+ for each organelle. • They show high sensitivity, low pH dependency, and negligible cytotoxicity. • They can monitor the crosstalk among metal ions using multicolor TPM imaging. [ABSTRACT FROM AUTHOR]