It is extremely challenging to quantitate lumenal Ca<sup>2+</sup> in acidic Ca<sup>2+</sup> stores of the cell because all Ca<sup>2+</sup> indicators are pH sensitive, and Ca<sup>2+</sup> transport is coupled to pH in acidic organelles. We have developed a fluorescent DNA-based reporter, CalipHluor, that is targetable to specific organelles. By ratiometrically reporting lumenal pH and Ca<sup>2+</sup> simultaneously, CalipHluor functions as a pH-correctable Ca<sup>2+</sup> reporter. By targeting CalipHluor to the endolysosomal pathway, we mapped lumenal Ca<sup>2+</sup> changes during endosomal maturation and found a surge in lumenal Ca<sup>2+</sup> specifically in lysosomes. Using lysosomal proteomics and genetic analysis, we found that
catp-6, a Caenorhabditis elegans homolog of ATP13A2, was responsible for lysosomal Ca<sup>2+</sup> accumulation-an example of a lysosome-specific Ca<sup>2+</sup> importer in animals. By enabling the facile quantification of compartmentalized Ca<sup>2+</sup>, CalipHluor can expand the understanding of subcellular Ca<sup>2+</sup> importers.