Over the past decade, Australian, Norwegian and Russian marine surveys have collected integrated seismic, gravity and magnetic data in the southern Indian Ocean. The more than 350,000 line-km of new airborne and marine magnetic observations for the East Antarctic continental margin have been compiled into an improved definition of crustal magnetic anomaly patterns. This compilation provides important new constraints on the breakup processes and igneous activity related to the formation of the passive margin of East Antarctica. The eastern sector of the map from Bruce Rise in the west to the D'Urville Sea in the east is largely dominated by seafloor spreading magnetic anomalies. The ‘Adélie Rift Block’ of highly stretched and extensively faulted continental crust is associated with a smooth anomaly fabric. Abrupt magnetic anomaly changes along the oceanic-continent transition in the Cooperation Sea including the Enderby Basin Anomaly extend for more than 1680 km from the Kerguelen Plateau towards the Cosmonaut Sea. Three sectors of the East Antarctic continental margin exhibit pronounced disparities in the anomaly patterns that strongly suggest different modes of seafloor formation. Strong positive seafloor magnetic anomalies mark the southern margin of the Kerguelen Plateau, the Maud Rise and adjacent areas in the Riiser-Larsen Sea. The new compilation suggests that at least 300 km of the Enderby Basin and Shackleton Basin may be part of the Cretaceous Kerguelen Volcanic Province and possibly maps an abandoned ‘fossil’ spreading center in the central Enderby Basin. The majority of the published age models for the Enderby Basin and “Australian sector” of the East Antarctic margin are not in agreement with the structural grain of magnetic anomalies in the newly compiled map.