Sea of Galilee (Lake Kinneret) is located in northern Israel in the area of complex tectonic setting where the Dead Sea Transform crosscuts other fault systems. Practical absence of wells in the sea hinders geological-geophysical data interpretation. Map of the total magnetic field shows an intricate pattern of the magnetic field distribution caused by a combined influence of the basalt flows of various age and magnetization in and around the sea. The identified magnetic anomalies were analyzed using methods of quantitative interpretation specially developed for complex geological conditions. The paleomagnetic stratigraphy of basalt associations around the Sea of Galilee basin proved to be correlated with the paleomagnetic zones in the sea. For the first time was developed the detailed magnetic-paleomagnetic scheme with K-Ar dating unmasking structure of magnetic anomalies in the sea and coordinating the revealed peculiarities with the surrounding anomalies.