Herein, a novel analytical method was reported for sensitive and selective quantification of malachite green (MG) in tap water and carp samples based on a combination of surface-enhanced Raman spectroscopy (SERS) and molecular imprinting technology. For this purpose, surface molecularly-imprinted magnetic nanoparticles (MIP@Fe3O4 NPs) were synthesized through recently developed living/controlled radical polymerization mechanism referred to as reversible chain transfer catalyzed polymerization (RTCP). Surface characterization of MIP@Fe3O4 NPs was carried out in detail by using the combination of several analytical techniques and the results showed the presence of a thin polymer layer on the nanoparticles. Rebinding properties, selectivity and reusability of the nanoparticles were investigated and the obtained results indicated the prepared nanoparticles had excellent selectivity, high adsorption capacity, fast adsorption kinetics and multiple-uses with an imprinting factor of 3.86. Then, silver dendrites (Ag NPs) were deposited on silicon wafers and used as SERS sensing platform. Moreover, surface properties of the SERS substrate were also investigated in detail in terms of stability, reusability and homogeneity. After that, the eluted MG from the imprinted nanoparticles was dropped on the sensing platform and SERS analysis was carried out. Under optimized conditions, limit of detection and limit of quantification were determined to be 1.50 pM and 4.96 pM for tap water, respectively and 1.62 pM and 5.38 pM for carp samples, respectively within acceptable recovery rates and standard deviations. The overall results indicated that the proposed method can be effectively used for the quantification of trace amounts of MG in tap water and carp samples. Moreover, the proposed method is promising for development of new ways to prepare MIPs via surface-initiated RTCP.