Intracellular calcium ion (Ca2+) signaling is heavily involved in development, as illustrated by the use of a number of Ca2+indicators. However, continuous Ca2+patterns during morphogenesis have not yet been studied using fluorescence resonance energy transfer to track the Ca2+sensor. In the present study, we monitored Ca2+levels during zebrafish morphogenesis and differentiation with yellow cameleon, YC2.12. Our results show not only clear changes in Ca2+levels but also continuous Ca2+patterns at 24 hpf and later periods for the first time. Serial Ca2+dynamics during early pharyngula period (Prim-5-20; 24–33 hpf) was successfully observed with cameleon, which have not reported anywhere yet. In fact, high Ca2+level occurred concurrently with hindbrain development in segmentation and pharyngula periods. Ca2+patterns in the late gastrula through segmentation periods which were obtained with cameleon, were similar to those obtained previously with other Ca2+sensor. Our results suggested that the use of various Ca2+sensors may lead to novel findings in studies of Ca2+dynamics. We hope that these results will prove valuable for further research in Ca2+signaling.