Geophysical surveys of the oceanic crust indicate that hydrothermal circulation universally occurs in seismic layer 2, which results in a low seismic velocity and high VP/VS due to the occurrence of cracks. However, the anomalously low VP/VS observed at the layer 2/3 transition cannot be explained by the crack model, because the effective medium theory predicts an increase in VP/VS due to crack development. In this study, we present the first evidence that shows the low VP/VS in the oceanic crust is caused by epidotization due to upward fluid flow in hydrothermal systems. Simultaneous measurements of elastic wave velocity and porosity of epidosites collected by the Oman Drilling Project show that quartz precipitation and spheroidal pores results in low VP/VS, in contrast to diabases that contain thin cracks. The presence of spheroidal pores in epidosites is supported by CT imaging, and is consistent with predictions from the effective medium model.