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We derive the microscopic spin Hamiltonian for rhombohedral CrI$_3$ using extensive first-principles density functional theory (DFT) calculations which incorporate spin-orbit coupling and Hubbard U. Our calculations indicate a dominant nearest-neighbor ferromagnetic Heisenberg exchange with weaker further-neighbor Heisenberg terms. In addition, we find a Dzyaloshinskii-Moriya interaction which primarily drives a topological gap in the spin-wave spectrum at the Dirac point, and uncover a non-negligible antiferromagnetic Kitaev coupling between the S=3/2 Cr moments. The out-of-plane magnetic moment is stabilized by weak symmetric bond-dependent terms and a local single-ion anisotropy. Using linear spin wave theory, we find that our exchange parameters are in reasonably good agreement with inelastic neutron scattering (INS) experiments. Employing classical Monte Carlo simulations, we study the magnetic phase transition temperature $T_c$ and its evolution with an applied in-plane magnetic field. We further demonstrate how future high-resolution INS experiments on the magnon dispersion of single crystals in an in-plane magnetic field may be used to quantitatively extract the strength of the antiferromagnetic Kitaev exchange coupling.