The Thracean-Aegean region was an area with mainly continental deposition during long time from the Late Oligocene to the Early Miocene. Sedimentological evidence from the roughly terrigeneous sediments testifies intensive uplift environments in the South Balkanids. Marine connections with the Mediterranean took place via the Pre-Alpine and Slovenian corridors during this time (Rögl, 1998; Popov et al., 2004).
The marine Middle Miocene sedimentation is very restricted in this region: S. Gillet (1957) illustrated Lower Sarmatian (Volhinian?) cardiids and Rückert-Ülkümen (1993) found foraminiferal assemblage with Sarmatian endemic species (such as Elphidium hauerianum) from the area west of İstanbul. The upper Sarmatian (Khersonian) Beds with Mactra caspia, M. bulgarica were described from the same area (Pamir, 1933; Erentoz, et al., 1953; Arıç-Sayar, 1957; Sayar, 1989). Probably, the region was a brackish water gulf of the Eastern Paratethys, extending to the Çanakkale region (Taner, 1997), but without continuation into the Aegean area. Data about the presence of Sarmatian and Maeotian in Macedonia (Stevanovic in Pontien, 1989; Stevanovic, Ilyina, 1982) are erroneous. Lagoonal fauna, of composition very similar to the Maeotian one, is alternated here with the real marine facies bearing Arca, big pectens and corals. Similar marine–brackish alternating facies are known in the Alçıtepe Formation outcropping in the northern Aegean, Gelibolu and Çanakkale regions (Sakınç & Yaltırak, 2005, Çağatay et al., 2006, 2007).
Brackish sediments with the Pontian-like mollusk and ostracod fauna are recognized in the whole Aegean Depression from the Northern Greece to Athens area. These deposits of the Choumnikon Formation are characterized by normal polarity and correspond to C3An.1n Subchron (6.30-6.04 Ma). The Choumnikon fauna includes numerous taxa with Paratethyan affinity: endemic lymnocardiines, Congeria and ostracods, but also euryhaline marine genera such as Cerastoderma and Mactra among mollusks, which were absent in the Pontian of Eastern Paratethys as well as in the Pannonian Basin. We believe that the origin of the Choumnikon brackish elements is related to the oldest Pannonian biota. This formation is 40-50 m thick, underlain and overlain by sediments with marine Mediterranean fauna. At the beginning of the Pontian (~ 6.0 Ma) this fauna populated the Eastern Paratethys. The Pontian brackish mollusks of the Eastern Paratethyan fauna comprised Congeria, Dreissena, Abra, inherited from the Maeotian time, and lymnocardiines (Pseudocatillus, Paradacna, Pontalmyra, Eupatorina, Euxinicardium), migrated to the Eastern Paratethys (Popov, Nevesskaya, 2000). Two last genera are unknown in the Pannonian Basin, but are present in the Aegean association. The species of the Late Pontian fauna inhabited the Mediterranen at the “Lago-Mare” stage (Esu, 2007).
At the same time, a few brackish basins existed in the Anatolian part with endemic non- Paratethyan fauna: Denizli Basin, in the western Anatolia, with Theodoxus, Micromelania, sculptural Valvata, Radix, Pseudocardita (Oppenheim, 1918; Taner, 1974a, b; Wesselingh et al. 2008) and Yalova Basin, (Yalakdere formation) in the Eastern Marmara region (Emre et al. 1998).
During the Pliocene continental environments prevailed again in the Thracean–Aegean region. However, earliest Zanclean Mediterranean transgression reached the northern Aegean, Dacic, and Taman basins (Çağatay et al. 2007; Maruntianu, Papaianopul, 1995; Semenenko, 1997).
Later, at the early-middle Quaternary time one-way connection prevailed and the Chaudian Didacna of Black sea origin was found in Çanakkale region (Andrussov, 1896; Taner, 1983), and Caspian Didacna subpyramidata Pravosl. was described from the middle Pleistocene of the Iznik lake basin (Islamoğlu, 2009). Late Pleistocene connections took place and were described in details based on microphytoplankton (Aksu et al., 1995, Mudie et al., 2002) and mollusks (İslamoğlu et al., 2001; Kazancı et al., 2004). In the latest Pleistocene (Neueuxinian), the Marmara basin was affected by only Paratethys, by interrupting the connection with the Mediterranean (İslamoğlu & Tchepalyga, 1998).