Outcrop sections from the Swiss Jura, consisting of carbonate-siliciclastic deposits spanning the Middle-Late Oxfordian boundary, provide a palaeogeographical cross-section ranging from coastal to shallow platform and intra-platform basin environments. Using a sedimentological and a 3rd order sequence stratigraphic framework based on those sections, the distribution of sedimentary organic matter (palynofacies) has been spatially studied in relation to sequence stratigraphy. The main factors influencing the spatial variations of sedimentary organic matter are the proximity of land, organic productivity, level of biodegradation and hydrodynamic conditions of the palaeoenvironment. These factors determine the distribution of the land-derived, relatively allochthonous organic constituents (phytoclasts, pollen and spores), and marine, relatively autochthonous constituents (phytoplankton and foraminifera linings). Five main palynofacies parameters appear as good indicators of proximal-distal trends: the relative proportion of total phytoclasts; the ratio of marine to continental palynomorphs; and the relative amount and species diversity of dinoflagellate cysts. In lowstand deposits, high-energy hydrodynamic conditions may affect these trends on the shallow platform, where storms tend to increase the proportion of the marine organic fraction landwards. These five palynofacies parameters are largely related to water depth. Therefore, when compared with the established 3rd order sequence stratigraphic framework, their stratigraphic variations indicate relative sea-level changes or, alternatively, proximality changes. Parameters indicative of more distal conditions increase in the transgressive and early highstand, and decrease in the late highstand. The opposite occurs for parameters indicative of more proximal conditions. Foraminifera linings seem to be particularly concentrated near the shelf edge and on the slope. Finally, bisaccate pollen may display cyclicity associated with alternating humid and dry periods. This palaeoclimatic signature may be related to orbital cyclicity.