The strong Agulhas Current and the weaker East Madagascar Current constitute the western boundary current system in the southern Indian Ocean. No persistent boundary current appears to exist in the Mozambique Channel west of Madagascar. The source region of the Agulhas Current south of Madagascar is characterized by a strong and swiftly-changing eddy field. Altimeter-derived near-surface geostrophic currents and high-resolution model simulations are used to identify typical flow patterns in the source region. It is shown that persistent mean current patterns exist which link the East Madagascar Current both with the Agulhas Current and through a retroflection with the South Indian Ocean Countercurrent. The eddy patterns display preferences for cyclonic and anti-cyclonic motion in certain areas. These favorite distributions are thought to originate from variations in the East Madagascar Current outflow south of the island. It is suggested that the changes are related to the interaction of the East Madagascar Current with the zonal band of strong eddies/waves which propagate from Australia westward and arrive at Madagascar near 25S.