Tissue development requires instructive input from multiple morphogenetic signals. To guide cellular decision making, cells must correctly integrate these diverse signals as well as coordinate behavior with their neighbors. Calcium (Ca2+) is a ubiquitous second messenger that plays important roles in many physiological activities such as fertilization, proliferation and apoptosis and is regarded as a central signal integrator. While extensive work has identified core components of Ca2+ signaling, the regulation between Ca2+ signaling and morphogen pathways is still poorly understood. Here we report a novel phenomenon of oscillating, intercellular Ca2+ transients (ICT) in Drosophila wing imaginal discs, and their relation to morphogen signaling. We found that the ICT exhibits a patterned behavior, both spatially and temporally. We have elucidated the Ca2+ pathway components that are responsible for ICT through a combination of genetic and chemical perturbations using an ex vivo imaging assay. We also demonstrated that Ca2+ dynamics are modulated by signaling pathways including Bone Morphogenetic Protein (BMP) and Hedgehog (Hh) signaling. These observations lead to a working model of Ca2+ signaling as a mediator of signal integration for morphogen pathways.