The hydrodynamic interaction of two floating bodies in waves freely floating or connected by a rigid link is studied by using a boundary element method in the frequency-domain. The exact two-body hydrodynamic coefficients of added mass, wave damping and exciting force are calculated from the radiation-diffraction potential solution of the improved Green integral equation associated with the free surface Green function. The irregular frequencies in the conventional Green integral equation make it difficult to predict the physical resonance of the fluid in the gap between two bodies floating side by side. However, the improved Green integral equation employed in this study is free of irregular frequencies and always yields the exact solution of the multi-body radiation-diffraction potential boundary value problem. The 6 degree-of-freedom motions of two bodies freely floating side by side or connected parallel by a rigid link have been calculated for the incident wave frequencies ranging from 0.1 to 5 radians per second in head, left and right bow quartering seas. The 6-component load of the rigid link have also been presented.