Vibronic coupling is a critical component of most mechanisms invoking quantum effects in biological processes. However, it is not clear how properties associated with vibrational coherence such as phase and coupling of atomic motion impact the efficiency of light-induced processes. Here, we show that deuteration of the H11-C11=C12-H12 double-bond of the 11-cis retinal chromophore in the visual pigment rhodopsin significantly and unexpectedly alters the photoisomerization yield. These results reveal a new vibrational phase-dependent isotope effect.