In the present work, we isolated tumidulin from the lichen Niebla sp., and found that (1) this lichen secondary metabolite displays inhibitory activity against CRC stemness, (2) mRNA levels of several cancer stem markers including ALDH1, CD133, CD44, Lgr5, and Musashi-1 are downregulated by tumidulin treatment, and (3) the Hh signaling pathway is involved in the suppression of Gli and SMO protein levels by tumidulin treatment. This evidence concerns the gene MSI1 and cancer.