A comparison of late Neogene planktic foraminiferal biogeography and stable isotopic records of shallow dwelling and deep dwelling planktic foraminifera from DSDP sites 214 (Ninetyeast Ridge, northeast Indian Ocean) and 586B (Ontong-Java Plateau, western Equatorial Pacific) provides a clue to the nature of the ocean circulation in the tropical Indo-Pacific during early Pliocene. The present study reveals that the late Neogene planktic foraminiferal data from the eastern and western sides of the Indonesian Seaway are very similar. The only distinct inter-ocean difference however is the absence of Pulleniatina spectabilis from the Indian Ocean. This species makes its first evolutionary appearance in the Equatorial Pacific at about 5.6 Ma (Early Gilbert reversed) and ranges up to 4.2 Ma (Top Cochiti subchron). The complete absence of Pulleniatina spectabilis from the Indian Ocean is attributed to blocking of westward flow of tropical waters of the Pacific to the Indian Ocean resulting in a major change in ocean circulation in the tropical Pacific and Indian oceans during 5.6 to 4.2 Ma. In order to understand the nature of this blockage, isotopic depth ranking of selected planktic foraminifera was carried out which reveals that the Indonesian Seaway became an effective biogeographic barrier to deep dwelling planktic foraminifera and thus it may be interpreted that the shallow sills that mark the Seaway in modern times were present as early as 5.6 Ma. The distribution of Pulleniatina spectabilis throughout the Equatorial Pacific reveals that Modern Equatorial Pacific Under Current (Cromwell Current) flowing towards east at a depth of 200-300 m (which is also the depth habitat of Pulleniatina spectabilis) was present at the beginning of the Pliocene (5.6 Ma). As a sequel to the blocking of the Indonesian Seaway and the resultant interruption in the flow of central Equatorial Current System of the Pacific to the west there was an increase in the western Pacific Warm Pool Waters and strengthening of the gyral circulation in the Pacific and Indian Oceans. This eventually triggered the intensification of the Asian Monsoon System.