Pseudotachylytes found in exhumed accretionary complexes are important for understanding earthquake faulting in subduction zones. However, frictional melting processes in a subduction zone fault under wet conditions remain poorly understood, mainly because of subsequent hydrothermal alteration. Here we present major- and trace-element and Sr isotope compositions of dark veins in a pseudotachylyte-bearing fault zone in the Shimanto accretionary complex, Japan. The dark veins show extreme enrichment in many trace elements and a normative orthoclase, irrespective of the preservation of a glassy matrix. Modeling shows that the pseudotachylytes contain 5.5× more melt fraction than expected from the abundance of matrix material in the host rock. These features indicate selective melting of a preexisting illite-rich shear zone. Rb-Sr isotope analyses show evidence for modification of the pseudotachylyte composition possibly through melt-clast fractionation during melting or subsequent processes. The distinctive geochemistry of the pseudotachylytes has been preserved even after hydrothermal alteration. Therefore, geochemical analyses are useful for evaluation of past frictional melting on faults particularly in subduction zones, and shed light on whether pseudotachylytes are rarely formed or merely rarely preserved.