The seafloor within the Perth Abyssal Plain (PAP), offshore Western Australia, is the only section of crust that directly records the early spreading history between India and Australia during the Mesozoic breakup of Gondwana. However, this early spreading has been poorly constrained due to an absence of data, including marine magnetic anomalies and data constraining the crustal nature of key tectonic features. Here, we present new magnetic anomaly data from the PAP that shows that the crust in the western part of the basin was part of the Indian Plate—the conjugate flank to the oceanic crust immediately offshore the Perth margin, Australia. We identify a sequence of M2 and older anomalies in the west PAP within crust that initially moved with the Indian Plate, formed at intermediate half-spreading rates (35 mm/yr) consistent with the conjugate sequence on the Australian Plate. More speculatively, we reinterpret the youngest anomalies in the east PAP, finding that the M0-age crust initially formed on the Indian Plate was transferred to the Australian Plate by a westward jump or propagation of the spreading ridge shortly after M0 time. Samples dredged from the Gulden Draak and Batavia Knolls (at the western edge of the PAP) reveal that these bathymetric features are continental fragments rather than igneous plateaus related to Broken Ridge. These microcontinents rifted away from Australia with Greater India during initial breakup at ~130 Ma, then rifted from India following the cessation of spreading in the PAP (~101–103 Ma).