A molecular detection method utilizing the magnetically induced aggregation of silver nanoparticle (NP)-embedded silica NPs for SERS activation is described. Here, silver embedded magnetic NPs (Ag-M-dots) composed of a magnetic core and silica shells, on whose surface silver NPs were formed, were used. Because the magnetic field induced aggregated Ag-M-dots exhibit a strong SERS signal compared to the dispersed Ag-M-dots, the system allows for the detection of adsorbed Raman label compound even at the 100 fM level. Adenine was tested as a model biocompound and its Raman spectrum could be observed at concentrations as low as 1 pM. The experimental results were supported by the theoretical calculations.