Based on a refined distribution chart of marine molluscan faunas of Japan in time and space, some key Neogene events in Japan are discussed with reference to those in the Pacific region. The Mid-Neogene climatic optimum around 16 Ma and a cooling of seawater temperature since 15 Ma are considered to be of Pan-Pacific scale. The opening of the Sea of Japan began around 16 Ma, simultaneously with the climatic optimum. Two tectonic events, the closing of the Indonesian Seaway and of the Central American Seaway possibly caused episodes of warm seawater temperatures on the Pacific side of Japan at 6 Ma and 3 Ma, respectively. The Izu Peninsula on the Pacific side of central Japan was a volcanic island in the tropical Pacific in Early Miocene time. During the northward drift of the island, relict species of Lepidocyclina manifested an evolutionary change and lasted until 5 Ma. Biotic evolutionary accelerations found in some endemic mollusca of Japan since 3 Ma are most likely due to phased drops of seawater temperature.