On Crete, Waynea cretica is found in the thermo- to the meso-mediterranean belts at altitudes between . These regions typically contain humid forest communities in ravines and canyons. The lichen has been recorded on the bark of Acer sempervirens, Old World sycamore (Platanus orientalis), and kermes oak (Quercus coccifera). Waynea cretica has since been recorded in several location in Algarve, Portugal.
