Cells possess multiple Ca(2+) stores and their selective mobilization provides the spatial-temporal Ca(2+) signals crucial in regulating diverse cellular functions. Except for the inositol trisphosphate (IP(3))-sensitive Ca(2+) stores, the identities and the mechanisms of how these internal stores are mobilized are largely unknown. In this study, we describe two Ca(2+) stores, one of which is regulated by cyclic ADP-ribose (cADPR) and the other by nicotinic acid adenine dinucleotide phosphate (NAADP). We took advantage of the large size of the sea urchin egg and stratified its organelles by centrifugation. Using photolysis to produce either uniform or localized increases of cADPR and NAADP from their respective caged analogs, the two separate stores could be visually identified by Ca(2+) imaging and shown to be segregated to the opposite poles of the eggs. The cADPR-pole also contained the IP(3)-sensitive Ca(2+) stores, the egg nucleus and the endoplasmic reticulum (ER); the latter was visualized using Bodipy-thapsigargin. On the other hand, the mitochondria, as visualized by rhodamine 123, were segregated to the opposite pole together with the NAADP-sensitive calcium stores. Fertilization of the stratified eggs elicited a Ca(2+) wave starting at the cADPR-pole and propagating toward the NAADP-pole. These results provide the first direct and visual evidence that the NAADP-sensitive Ca(2+) stores are novel and distinct from the ER. During fertilization, communicating signals appear to be transmitted from the ER to NAADP-sensitive Ca(2+) stores, leading to their activation.