The magnetic environment may influence the functioning of the cardiovascular system. It was reported that low-frequency and static magnetic fields affect hemodynamics, heart rate, and heart rate variability in animals and humans. Moreover, recent data suggest that magnetic fields affect the circadian rhythms of physiological processes. The influence of the magnetic environment on heart functionating during early development has been studied insufficiently. We utilized transparent zebrafish embryos to evaluate the effect of the hypomagnetic field on the characteristics of cardiac function using a noninvasive optical approach based on photoplethysmographic microscopic imaging. The embryos were exposed to the geomagnetic and hypomagnetic fields from the second to the 116th hour post fertilization under a 16 h light/8 h dark cycle or constant illumination. The exposure of embryos to the hypomagnetic field in both lighting modes led to increased embryo mortality, the appearance of abnormal phenotypes, and a significant increase in the embryo’s heartbeat rate. The difference between maximal and minimal heartbeat intervals, maximal to minimal heartbeat intervals ratio, and the coefficient of variation of heartbeat rate were increased in the embryos exposed to the hypomagnetic field under constant illumination from 96 to 116 h post fertilization. The dynamics of heartbeat rate changes followed a circadian pattern in all studied groups except zebrafish exposed to the hypomagnetic field under constant illumination. The results demonstrate the importance of natural magnetic background for the early development of zebrafish. The possible mechanisms of observed effects are discussed.