Recently the case which pressure fluctuation enlarges with high partial load of the Francis turbine is reported. In this study, model test was conducted to investigate this instability vibration. When the instability vibration occurred, large pressure fluctuation those frequency is about 40 Hz occurred at casing and between runner and guide vane. On this condition, cross-section of the whirl is oval and the whirl rotates in the whirl core circumference at about 20 Hz. So the oval cross section whirl knocks the wall surface twice in 1 round and the frequency is about 40 Hz. This frequency is near the dominant frequency at casing inlet and between runner and guide vane. It is thought to be the instability vibration is caused by this oval cross section whirl.