Based on Bayesian modeling procedure, a stochastic procedure is introduced. Using this procedure, directional wave spectra can be estimated by using the ship motion data which were recorded during the ship underway. The prior distribution in this procedure consists of two parts. The one is a stochastic constraint so called Gaussian smoothness prior distribution. And the other one is adopted to avoid excessive estimation for the directional wave spectra. Furthermore, the encounter frequencies are transformed into the true wave frequencies even in following seas. In order to examine the reliability of the proposed procedure, the onboard tests were carried out. And, the possibility of this procedure can be shown and problems encountered on applying are reported.