The Mytilinii Basin, eastern Samos Island, Greece, is one of many basins that developed in southeastern Europe during the Upper Neogene. The oldest lacustrine portion is of Late Miocene age, and besides tuffs, includes bituminous limestones, marlstones, dolostones and porcelanites of the Pythagorion Formation, and the limestones and diatomites of the overlying Hora Beds. Younger sedimentary rocks of Turolian through Pliocene age partially covered the Pythagorion Formation and Hora Beds (PFHB). Diatom floras range from well preserved to highly corroded and from sparse to abundant. The main taxa include Cyclotella aegaea, C. aegaea var. pythagoria, an unidentified Cyclotella and Nitzschia frustulum, and less common Epithemia turgida, E. reichelti, Synedra ulna, Tryblionella granulata, Encyonema silesiaca, Diploneis ovalis and Cocconeis placentula. Chrysophyte cysts, Hydrobia molluscs and trace fossils occur sporadically. The environmental evolution of the PFHB can be divided into three major stages. Fluctuating shallow to deeper waters in a saline lake characterized Stage A. Saline lake and playa environments with evidence for frequent earthquake events in the form of convolute bedding, drape folds and brecciated sediments characterized Stage B. During Stage C, the lake may have partially or completely split into two separate lakes. In the southeast, a saline playa passed laterally into a deeper-water lake. Locally, fresher-water ponds occurred. Subsequently, a deeper, possibly oligotrophic lake developed. In contrast, a saline lake with abundant diatoms formed in the northwest of the basin, in which diatom blooms led to whiting events and deposition of carbonate laminae. Cyclotella dominated the early floras in this water body, with later assemblages being co-dominated by Cyclotella and Nitzschia frustulum, possibly reflecting seasonal changes. Sedimentation was terminated by uplift and (or) increasing aridity associated with the Messinian Salinity Crisis.