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Shallow sediment lithology and stratigraphy were investigated at selected areas off Santa Maria di Leuca (SML) on the Apulian margin between 350 and 1200 m water depth, in order to define the sea-bottom character on which coral mounds have developed. According to existing geophysical data and in-situ observations, deep coral growth in the SML area creates patches of colonies typically settled on hard substrates on the upper flanks and/or near the top of mound-like structures and elongated ridges. The sedimentary stratigraphy is strongly influenced by the local topography, which is modeled by tectonic and geomorphological forcing: large-scale erosional features, slope failure and sediment mass accumulation are evident from seismic investigations. Additionally, sites of preferential sediment accumulation due to the action of bottom currents are identified. As a result, a complex sedimentary pattern characterizes this part of the Apulian margin, with strong lateral variability in sediment type and age. Although hemipelagic silty clay constitutes the main lithology, there are sites characterized by periodic accumulation of silt and fine sand and local re-deposition of coarse biogenic sand from the surrounding areas and from shallower depths. Excluding one site, where mid-Pleistocene sediments are brought very close to the bottom-surface due to wide-scale erosion, all collected sediments are late Pleistocene to Holocene in age and fall biostratigraphically within the Emiliania huxleyi acme nannofossil zone. Reworking, detected through nannofossil analysis, is common in most cores, excluding the ones taken from topographic highs, and is variable in extent from site to site and within the sediment column; it includes Cretaceous to Early Pleistocene species, suggesting provenance from extended successions or various stratigraphic levels, outcropping on the submerged Apulian margin or in adjacent land sections. Reworking is often associated with a high content of lithogenic particles and an increase in the coarser (silt) fraction. Coral debris was collected at many stations, both at the sediment surface and within the stratigraphic sequence, with varying abundance in relation to proximity to the coral colonies. Radiometric dating and micropaleontological analyses at some sites allow us to propose a sequence of coral colonization phases.