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Chemostratigraphy uses chemical fingerprints stored in sediments and sedimentary rocks for stratigraphic correlation. Stable isotope signatures fixed in sedimentary inorganic and organic matter are among the most powerful methods used in chemostratigraphy. This study focuses on the use of oxygen and carbon isotope geochemistry in stratigraphy. The importance of oxygen isotope stratigraphy for paleocliamte research is documented in case study I. Oxygen isotope stratigraphy can be used to trace climate pulse through the last few million years. It serves also as a tool for reconstruction of multicentennial climate variations on a global scale. Case study II demonstrates how carbon isotope stratigraphy in Cretaceous successions is used for correlation between ammonite dated section and sections dated with magnetostratigraphy. Case study III focuses on the use of carbon isotope stratigraphy in the Paleozoic. Carbon isotope studies have been intensively used in the Paleozoic to unravel changes in the global carbon cycle and for chemostratigraphic correlation of sections from various palaeocontinents. However, diagenesis is a major concern since Palaeozoic carbonates may have been affected by intense recrystallisation and considerably higher temporal overprint in comparison to Mesozoic or Cenozoic carbonate sequences. Reliable Paleozoic carbon isotope curves are generally based on the analysis of brachiopod shells