Recent progress in the realization of magnetic GaAs nanowires (NWs) doped with Mn has attracted a lot of attention due to their potential application in spintronics. In this work, we present a detailed Raman investigation of the structural properties of Zn doped GaAs (GaAs:Zn) and Mn-implanted GaAs:Zn (Ga0.96Mn0.04As:Zn) NWs. A significant broadening and redshift of the optical TO and LO phonon modes are observed for these NWs compared to as-grown undoped wires, which is attributed to strain induced by the Zn/Mn doping and to the presence of implantation-related defects. Moreover, the LO phonon modes are strongly damped, which is interpreted in terms of a strong LO phonon-plasmon coupling, induced by the free hole concentration. Moreover, we report on two new interesting Raman phonon modes (191 and 252 cm −1) observed in Mn ion-implanted NWs, which we attribute to Eg (TO) and A1g (LO) vibrational modes in a sheet layer of crystalline arsenic present on the surface of the NWs. This conclusion is supported by fitting the observed Raman shifts for the SO phonon modes to a theoretical dispersion function for a GaAs NW capped with a dielectric shell. © 2019 IOP Publishing Ltd.