The role of the Indonesian Throughflow (ITF) in the thermocline circulation of the low-latitude Pacific Ocean is explored using a high-resolution primitive equation ocean circulation model. Seasonally forced runs for a domain with an open Indonesian passage are compared with seasonally forced runs for a closed Pacific domain. Three cases are considered: one with no throughflow, one with 10 Sv of imposed ITF transport, and one with 20 Sv of ITF transport. Two idealized tracers, one that tags northern component subtropical water and another that tags southern component subtropical water, are used to diagnose the mixing ratio of northern and southern component waters in the equatorial thermocline. It is found that the mixing ratio of north/south component waters in the equatorial thermocline is highly sensitive to whether the model accounts for an ITF. Without an ITF, the source of equatorial undercurrent water is primarily of North Pacific origin, with the ratio of northern to southern component water being approximately 2.75 to 1. The ratio of northern to southern component water in the Equatorial Undercurrent with 10 Sv of ITF is approximately 1.4 to 1, and the ratio with 20 Sv of imposed ITF is 1 to 1.25. Estimates from data suggest a mean mixing ratio of northern to southern component water of less than 1 to 1. Assuming that the mixing ratio changes approximately linearly as the ITF transport varies between 10 and 20 Sv, an approximate balance between northern and southern component water is reached when the ITF transport is approximately 16 Sv. It is also shown that for the isopycnal surfaces within the core of the equatorial undercurrent, a 2°C temperature front exists across the equator in the western equatorial Pacific, beneath the warm pool. The implications of the model results and the temperature data for the heat budget of the equatorial Pacific are considered.