A new aeromagnetic survey of the Junction Magnetic Anomaly in northern New Zealand reveals that it is associated with up to 10 subparallel lineaments. The Junction Magnetic Anomaly delineates the Dun Mountain Ophiolite Belt, a remarkably linear though sigmoidally bent major boundary zone traceable through most of New Zealand, which separates terranes sutured onto the New Zealand Gondwana margin in late Mesozoic time. Modelling of the lineaments, in conjunction with a new review of structures along the Dun Mountain Ophiolite Belt throughout New Zealand, indicates that the Dun Mountain Ophiolite Belt in Auckland consists of a number of imbricate slices, most of which are likely to dip steeply to the east (i.e. overturned away from the former trench) and extend to considerable depth in the crust. The source bodies for the central high-amplitude magnetic lineaments are interpreted to be serpentinite shear or mélange zones, cutting a large lensoid body of ultramafic rocks, similar to those occurring elsewhere along the length of the Dun Mountain Ophiolite Belt. Our data have revealed that a formerly postulated offset of the Dun Mountain Ophiolite Belt in the region instead resembles a duplex or thrust imbricate-like bundling of shear zones. These shear zones were probably initiated as accretion thrusts, but complexities in their pattern indicate subsequent shearing, including ‘backfolding’ to an overturned attitude and possibly strike slip to produce the linear nature of the Dun Mountain Ophiolite Belt. The outer lineaments mostly mark accretion thrusts in the adjacent terranes. This study demonstrates that detailed aeromagnetic surveys can delineate the fine structure in ophiolite complexes and thereby give valuable insights into the effects of micro-continental collision on an accretionary margin.