Development of highly sensitive molecular sensors is of immense current interest for biomedical diagnosis. Although the possibility of single molecule detection through plasmonic sensors based on surface enhanced Raman scattering (SERS) has been demonstrated, the practical application of such devices is hindered due their complex fabrication strategies and inhomogeneous Raman signal response. Here we present a simple biological method for large scale fabrication of plasmonic microtubes using selective nonpathogenic fungi as living templates. The biologically fabricated microstructures can be used as SERS substrates for the detection of organic molecules with signal enhancement factors as high as 1 × 1010, exploiting their rugged, highly porous surfaces with intense hot spots. Although they are structurally not as perfect as those of chemically or physically fabricated plasmonic SERS substrates, their morphological/geometrical inhomogeneity introduces only about a one order fluctuation of SERS enhancement factor along their lengths. The plasmonic microstructures have great potential for the fabrication of cheap, efficient, and highly sensitive gold-based biosensors for the detection and monitoring of organic molecules.