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Sediments from two deep-sea bottom cores from the Myrtoon basin in the SW Aegean Sea and Eastern Cretan Sea were examined by quantitative mineralogical and geochemical analysis to infer sediment provenance and climatic conditions and palaeo-environmental control on sediment deposition. Both cores contain calcareous muds and silts with dark olive-grey organic rich intervals corresponding to the regional sapropel S1 horizon. The presence of a few tephra layers documents volcanic activity in the southern part of the Aegean Sea. The bulk sediments contain abundant carbonate minerals (mainly calcite and Mg-calcite) and clay minerals (mainly illite and smectite) and accessory serpentine, talc and hornblende, which attest to contributions from ultrabasic sources. There is a sharp decrease of the Mg-calcite content and the Mg/Ca ratio of the carbonate fraction in sapropelic sediments followed by an increase of the average grain size. A well expressed negative relationship between illite and smectite was observed in the clay fraction in full accordance with previous studies. However, this trend is absent from the bulk sediments, because smectite is significantly overestimated in the oriented clay fractions. Clay mineral distribution is controlled mainly by sediment sorting, with deposition in the sapropelic sediments being also affected by climatic changes. The different types of smectite in the cores and the presence of smectite with high dehydroxylation temperature in the SE Aegean, suggests that the sediment supply from SE Mediterranean sources should be limited. (C) 2019 Elsevier B.V. All rights reserved.