The mesophotic domain is a poorly explored part of the oceans, notably in the Mediterranean Sea. Benthic communities in these depths are not well documented and as such are under higher risk from anthropogenic impacts. Hard substrate habitats in this depth window are not common and are a key ecotope. The Malta Plateau in the central Mediterranean, which is characterised by low sedimentation rates, offers a potentially unexplored domain for these features. Bathymetric and backscatter data offshore of the eastern coast of the island of Malta were used to characterise the benthic habitats. >1700 small structures were identified in mesophotic depth and verified by dives to be biogenic mounds. These mounds extend from several meters to tens of meters in diameter and occur in two main depth windows 40 to 83 mbpsl and 83 to 120 mbpsl, each formed probably in a different stage along the last glacial cycle. The mounds are composed of interlocking bioconstruction by encrusting organisms and are colonised by sponges and various cold water corals (most of which are protected). This unique and important habitat is currently under grave threat by human activity, most immediately by trawling activity.