The Seyitomer coal deposit is an important source of energy in Turkey. This study aims to determine mineralogical, geochemical characteristics, and genesis of clays associated with coal seams in order to identify their precipitation environment. The Late Miocene-Pliocene units comprise organic-rich shale, organic-rich marl, marl, coal seam, siltstone and sandstone deposited in a fluvial and lacustrine environment, with associated tuff and tuffite in the Seyitomer coal deposit. Serpentinite, sandstone, organic-rich shale and tuffaceous host rocks of the coal deposit are partly to completely argillized and partially carbonate cemented having also stockwork type silica in fill fissures. Smectite, illite, and kaolinite are associated with quartz, feldspar, olivine, gypsum and pyrite. Oriented flaky illite with irregular outlined kaolinite, and smectite flakes edging and coating relict feldspar and volcanic glass grains developed by a dissolution-precipitation mechanism in an alkaline micro-environment during deposition and diagenetic process. The occurrence of subrounded microorganisms on resorbed feldspar and the coexistence of smectite/illite flakes with organic matter, pyrite, and siderite indicates that degradation of feldspar and devitrification of volcanic glass is biologically mediated. The slight enrichment of heavy rare earth elements (HREE) compared to light rare earth elements (LREE) with a positive Eu and Ce anomalies reflects fractional crystallization of feldspar and amphibole. Alteration of feldspar, biotite, serpentine and volcanic glass resulted in the concentration of Al, Fe, Mg, and K in a stagnant environment and precipitation of beidellitic smectite and illite in an alkaline environment. Kaolinite precipitated in an acidic open hydrological system. An increase in Ni/Co and V/ (V + Ni) ratios in altered units also suggest anoxic and anoxic to dysoxic conditions. Occurrence of Pityosporites microalatus (Pinus), Laevigatosporites haardti, Pityosporites spp., Polyvestibulopollenites verus (Alnus), Compositae and Graminae in the Seyitomer coal deposit suggest subtropical to warm-temperature humid climate during Late Oligocene-Middle Miocene period. Association of argillization and silicification with coal, microorganisms, pyrite, and gypsum indicates a swampy environment and partial hydrothermal processes. This interpretation is corroborated by the calculated formation temperatures from stable-isotope analysis of 30-463 degrees C for smectite and 140-156 degrees C for illite. The high delta S-34 isotope values (16.8-33.3%.) indicate a mixed diagenetic and hydrothermal origin for the sulphide and sulfate minerals. (C) 2017 Elsevier B.V. All rights reserved.