Surface-enhanced Raman spectroscopy (SERS) is a promising optical method for analyzing molecular samples of various nature. Most SERS studies are of an applied nature, indicating a serious potential for their application in analytical practice. Dendritelike nanostructures have great potential for SERS, but the lack of a method for their predictable production significantly limits their implementation. In this paper, a method for controllably obtaining spatially separated, self-organized, and highly-branched silver dendrites via template synthesis in pores of SiO2/Si is proposed. The dendritic branches have nanoscale roughness, creating many plasmon-active “hotspots” required for SERS. The first held 3D modeling of the external electromagnetic wave interaction with such a dendrite, as well as experimental data, confirms this theory. Using the example of a reference biological analyte, which is usually used as a label for other biological molecules, the dendrites’ SERS-sensitivity up to 10−15M was demonstrated with an enhancement factor of 108. The comparison of simulation results with SERS experiments allows distinguishing the presence of electromagnetic and chemical contributions, which have a different effect at various analyte concentrations.