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Plant hormones and light signals enable plants to respond to changes in their environment. These stimuli are perceived by receptors that transmit responses to the inside of cells by inducing changes in cytoplasmic concentrations of chemical messengers, such as calcium. Many plant hormone and light signals cause elevations in the cytoplasmic calcium concentration. Recent studies are reviewed here that reveal how genetic mutations disrupt stimulus-induced calcium elevations in plant cells. These studies provide genetic evidence for the importance of calcium as a second messenger in plant signal transduction. A classical question has remained unanswered until recently, namely, how can different stimuli use the same second messenger, calcium, to mediate different responses in plants? Recent research and models are reviewed here that show several important mechanisms contributing to specificity in calcium signaling in plant cells. These mechanisms include (i) the activation of different calcium channels in the plasma membrane and organellar membranes of plant cells; (ii) the specific frequencies needed by calcium oscillations to mediate specific responses; (iii) the differential responses of different cell types to the same stimulus; and (iv) within each cell, the importance of intracellular localization of calcium gradients and calcium elevations to elicit the response. These advances show that plant cells contain a sophisticated apparatus that allows them to respond to many different environmental conditions through the second messenger, calcium.