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. Plain Language Summary The low velocity and high VP/VS structure in the upper oceanic crust (“seismic layer 2”) is generally associated with the development of fluid‐filled thin cracks. However, the anomalously low VP/VS ratios that have been observed in the layer 2/3 transition cannot be explained by the classical thin crack model. We provide the first direct evidence of low VP/VS ratios in epidotized rocks that are associated with the occurrence of spheroidal pores and quartz precipitation. Our theoretical calculations show that both the crack geometry and alteration minerals are required to explain the anomalously low VP/VS ratios in the transition zone. Knowledge of these unique physical properties of epidotized rocks will facilitate the detection of fluid upwelling zones in the oceanic crust, which are possibly linked to the hydrothermal ore resources. Key Points Epidosites are characterized by low VP/VS due to the presence of spheroidal pores Low VP/VS anomaly in the layer 2/3 transition can be explained by alterations and pore development during epidotization The unique characteristics of epidosites may be useful to detect the fluid upwelling zones in the oceanic crust