The present study examines variation of tropical cyclone (TC) activity in the South Indian Ocean (SIO) during TC seasons (December–March) for the period 1979–2004. The impact of the El Niño–Southern Oscillation and the Madden-Julian Oscillation (MJO) on the variation is revealed through a composite analysis. During El Niño periods TC genesis was shifted westward, enhancing the formation west of 75°E and reducing it east of 75°E. These changes in the genesis correspond to a westward shift of convection. It may be explained by a remote effect on the SIO; that is, the increase in sea surface temperature in the central eastern Pacific alters the Walker circulation and forms an anomalous anticyclonic circulation in the east SIO during El Niño. The spatial difference in TC passages between El Niño and La Niña shows a significant decrease to the southeast of Madagascar but a moderate increase in the central midlatitude SIO, indicating that TCs move farther east during El Niño. This change is possibly due to the anomalous southwesterlies east of Madagascar. Variation of TC activity also depends on various MJO phases: frequent TC passages for phases 2–4 (strong convective activity straddles along the equatorial Indian Ocean) versus infrequent TC passages for other phases. TC tracks tend to be more south oriented in phase 3 compared with those in phases 2 and 4. This is possibly caused by the increased steering northerlies which are a part of the anticyclonic Rossby wave of Gill type in response to the suppressed MJO-related convection in the maritime continent.