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Seasonal variability of the depth-integrated transport in the Indonesian Seas is investigated in detail, together with its driving mechanism, by use of an Indo-Pacific ocean general circulation model that allows the circulation around Australasia. Modeled net throughflow shows an annual mean transport of 9.5 Sv from the Pacific to the Indian Ocean with a maximum (minimum) transport of 11.6 Sv (6.0 Sv) in August (January). Seventy-five percent of this transport flows through the Lombok Strait in the present model. Comparison with the result of Masumoto and Yamagata [1993], in which the circulation around Australasia was not permitted, clarifies that the magnitude of the net interbasin throughflow does not affect the seasonal variations in the depth-integrated transport through the Lombok Strait. Several additional experiments are also carried out by masking winds over particular regions to identify which part of winds is actually effective in the seasonal variations in the depth-integrated transport through the Timor Sea as well as the Lombok Strait. It turns out that the seasonal variability of the transport through the Lombok Strait is almost perfectly governed by the winds over the equatorial Indian and Pacific Oceans. On the other hand, the coastally trapped waves generated by the winds along the western and southern coast of Australia play an important role in the seasonal transport variation through the Timor Sea.