Perturbation theory is used systematically to investigate the symmetries of the Dirac Hamiltonian and their breaking in atomic nuclei. Using the perturbation corrections to the single-particle energies and wave functions, the link between the single-particle states in realistic nuclei and their counterparts in the symmetry limits is discussed. It is shown that the limit of S-V=const and relativistic harmonic oscillator (RHO) potentials can be connected to the actual Dirac Hamiltonian by the perturbation method, while the limit of S+V=const cannot, where S and V are the scalar and vector potentials, respectively. This indicates that the realistic system can be treated as a perturbation of spin-symmetric Hamiltonians, and the energy splitting of the pseudospin doublets can be regarded as a result of small perturbation around the Hamiltonian with RHO potentials, where the pseudospin doublets are quasidegenerate.