Abstract We studied two middle Pleistocene terraced deposits exposed along the Trani cliff and at Coppa Nevigata in the Apulia region, southern Italy. In particular, our study focused on stromatolitic units that are present at two sites. At the Trani cliff, Unit I consists of cemented, whitish, fine-grained, massive or bedded limestone. The limestone grades upwards into massive, porous bioconstructed calcareous bodies composed of in situ Charophyta stems and/or stromatolites. The uppermost part of the unit is composed of whitish calcarenite/calcisiltite layers with Characeae. The interpreted sedimentary environment for this unit is a hypersaline-brackish lagoon. At Coppa Nevigata, the NVI unit is composed of tawny or yellow ochre sand with rare polygenic centimetric pebbles. The sand grades upwards into light yellow and ochre sandy/clayey silt or clay. Some layers are cemented and form marly limestones which contains columnar stromatolites. The uppermost part of the unit consists of yellow ochre or tawny marly limestones and marls that are rich in external moulds of Abra sp. and Cerastoderma glaucum. The interpreted sedimentary environment for this unit is a brackish lagoon. Unit I and the NVI unit have been dated to MIS 9 and MIS 11, respectively, by applying the Amino Acid Racemisation (AAR) method to ostracod shells. The stromatolites of the NVI unit are ascribable to SH type, whereas those of Unit I are ascribable to SH and LLH types and to colloform type. In particular, the stromatolites at the Trani cliff are similar in shape and sedimentary environment to the modern stromatolites in Shark Bay (Australia). The water temperature and salinity conditions under which the current stromatolites live indicate that tropical/subtropical conditions were present in the Mediterranean Sea during MIS 11 and MIS 9. Our reconstructions suggest that: 1) during MIS 11, the sea surface temperatures (SSTs) were consistent with literature data, that indicate SSTs ∼3 C° higher than the current ones. 2) during MIS 9, the lagoon in which Unit I formed had a mean water temperature of the coldest month at least 10–12 C° higher than that in modern southern Adriatic and at least 3–4 C° higher than that in some modern north-African lagoons. Therefore, our study supports the hypothesis that the Mediterranean Sea experienced tropical/subtropical conditions during MIS 9 that were similar to those of MIS 11.