Abstract: Intraband cyclotron resonance (CR) transitions of a two-electron quantum dot containing a single magnetic ion is investigated for different Coulomb interaction strengths and different positions of the magnetic ion. In contrast to the usual parabolic quantum dots where CR is independent of the number of electrons, we found here that due to the presence of the magnetic ion Kohn's theorem no longer holds and CR is different for systems with different number of electrons and different effective electron-electron Coulomb interaction strength. Many-body effects result in shifts in the transition energies and change the number of CR lines. The position of the magnetic ion inside the quantum dot affects the structure of the CR spectrum by changing the position and the number of crossings and anticrossings in the transition energies and oscillator strengths.