The Wharton Basin in the Indian Ocean is one of the most extensively deforming ocean basins, as confirmed by the occurrence of several very large earthquakes starting from January 12, 2012 with Mw 7.2 followed by the great earthquakes of April 11, 2012 with Mw 8.6 and Mw 8.2. Although the Mw 7.2 and Mw 8.2 earthquakes seem to have ruptured the re-activated N–S striking fracture zones, the largest event (Mw 8.6) required the rupturing of several faults, oblique to each other, in a very complex manner. In order to understand the nature of deformation in these earthquakes rupture zones, we recently acquired 90 000 km2 of bathymetry, 11 400 km of sub-bottom profiling, gravity and magnetic data covering the rupture areas of the 2012 earthquakes east of the Ninety-East Ridge, in the northwestern Wharton Basin. These new data reveal six N8°E striking re-activated fracture zones (F5b, F6a, f6b, F7a, F7b and F8), where the fracture zone F6a can be followed for over 400 km and seems to be most active. The epicenters of the Mw 8.6 and Mw 8.2 earthquakes lie on the fracture zones F6a and F7b, respectively. The newly observed fracture F5b in the east is short, and has an extensional basin at its southern tip. The fracture zone F8 defines the eastern boundary of the Ninety-East Ridge. The presence of en echelon faults and pull-apart basins indicate left-lateral motion along these fracture zones. In between these fracture zones, we observe pervasive 290° striking right-lateral shear zones at 4–8 km intervals; one of which has cut through a seamount that might have ruptured during the Mw 8.6 earthquake. We also observe another N20°E striking left-lateral shear zones in the vicinity of F7b and F8, which is coincident with the strike of one of the nodal planes of the Mw 8.6 focal mechanism. These N20°E striking shear zones are interpreted as R Riedel shears and the N290°E striking shear zones as R′ Riedel shears. These shear zones are formed by a series of N335°E striking en echelon normal faults. Our data also show the presence of N65°E striking thrust faults east of the Ninety-East Ridge, orthogonal to the regional principal direction of compression. Furthermore, extensive bending-related faulting is also observed close to the Sumatra trench with normal faults also striking at N335°E, similar to the normal faults that form the shear zones. Normal faults with a similar orientation are also present at the southern tip of F5b. We explain all these observations with a single coherent model of deformation in the Wharton Basin, where a dominant part of the regional NW–SE compressional stress is accommodated along the N8°E re-activated fracture zones, and the rest is distributed along shear zones, thrust and normal faults between these fracture zones. The thrust and normal faults are orthogonal to each other and define the direction of principal compressive and extensive stresses in the region whereas the two shear zone systems form a conjugate pair.