Tree trunks were found in situ in Miocene strata of the Mydlovary Formation of the South Bohemian Basin. Our study presents microscopic and chemical tissue analyses of these tree trunks. The trees were fossilized and flattened. However, they are well preserved, which made the analyses feasible. Good preservation of the tissues is indicated by the high Tissue Preservation Index, the high content of cellulose, and the slightly gelified state of the wood. The Gelification Index indicated that there was only limited alteration during diagenesis. Huminite macerals prevailed over liptinite and inertinite macerals, and two varieties of ulminite and textinite were distinguished, differing in colour reflection, light fluorescence, and reflectance values. The biomarker composition in the extracts of the fossil wood obtained by gas chromatography-mass spectrometry, included terpenoid signatures, supporting a relationship to the Family Cupressaceae s.s.. Gradual burial of the trees is indicated by the fact that they lay crosswise on top of each other. The character of the sedimentary environment and the physiological differences of the trees could explain the deformation and the high degree of preservation.