This paper analyzed the trend in long-term change in annual mean equilibrium water temperatures and air temperatures all over Japan for 50 years (1963–2012), and investigated their regional characteristics. To analyze the time series data of the temperatures, Mann-Kendall test was used to statistically detect the trend and Sen’s slope was used to quantitatively evaluate its significance. The results showed that a tendency for temperature to rise in the equilibrium water temperature was common in the coastal part of the Pacific Ocean in the western part from the Kanto region. In these areas, a positive correlation was found in the rising tendency between the equilibrium water temperature and the air temperature. Furthermore, a trend towards lowering of temperature in the equilibrium water temperature was detected more often in the northern part of Tohoku and Kyushu regions as well as the coastal part of the Sea of Japan. In these areas, there was a negative correlation between the equilibrium water temperature and the air temperature.