The results of palynomorph biofacies analysis of the Lower and Middle Jurassic deposits of Western and Eastern Siberia are presented. A comprehensive study of different groups of palynomorphs (spores and pollens, dinoflagellate cysts, acritarchs, prasinophytes, Zygnematales algae, etc.) was carried out. Detailed analysis of the distribution of separate taxa and quantitative proportions of various groups of microphytofossils in sections of Western and Eastern Siberia allowed combinations of palynomorphs reflecting different facies types to be established. In total, nine ecological-facies associations were distinguished—from continental, coastal marine, and shallow-water to typical marine deep-water.