In Japan Agency for Marine-Earth Science and Technology (JAMSTEC), several autonomous underwater vehicles (AUVs) and a manned submersible SHINKA6500, which has a capability to dive up to the depth of 6,500 m, have been operated and contributed various scientific researches in deep water. These vehicles are equipped with vertical acoustic communication systems with the mothership. However, these systems have not been updated since they were built originally. Therefore, last year, a prototype of very high-rate communication system was developed, and its performance was verified in an at-sea experiment, with installed in SHINKAI6500. As results, the effective data rate of 69.24 kbps at highest was achieved from the depth of 3,600 m with no error using the frequency band of 10 kHz, that is, its spectral efficiency was 6.924 bps/Hz. The performance was very stable even under the effects of the fluctuation of the mothership and ascending/descending movement of the submersible, whose velocity was up to 2 knots approximately. Thus, it was demonstrated that the new developed communication system is very effective for vertical communication between an underwater vehicle and a mothership.