To monitor neuronal activities calcium imaging is one of the promising methods. We have been developing genetically encoded calcium indicators (GECIs) called G-CaMPs (green GECIs) and R-CaMPs (red GECIs). Because G-CaMPs and R-CaMPs are genetically encoded and their expression can be spatially and temporally controlled, G-CaMPs and R-CaMPs are particularly useful to monitor neuron- and glial-activities in vivo. To monitor neural activity in zebrafish, we expressed G-CaMP7a in the tectum, which is the visual center in the zebrafish brain, and performed calcium imaging under a fluorescent microscope. When a prey paramecium swam around a zebrafish larva expressing G-CaMP7a in the tectum, we could detect fluorescent increases in cell bodies and dendrites. We could functionally map the tectal-neuron activities according to the position of the paramecium. Recently we developed new R-CaMP called R-CaMP2. Using the calmodulin-binding sequence of CaMKK-α and CaMKK-β in lieu of an M13 sequence resulted in high affinity and threefold-faster kinetics of Ca2+ transients than the parental probe R-CaMP1.07. We expressed R-CaMP2 in C. elegans neurons and/or the body wall muscles (BWMs) and imaged their activities with a confocal microscope. We could monitor neuronal or musclular activities from freely-moving C. elegans. Next we generated transgenic C. elegans that expressed channelrhodopsin 2 and G-CaMP6 in GABA neurons and R-CaMP2 in the BMWs. We successfully achieved dual-color monitoring of neuronal and musclular activities in response to photostimulation.