ABSTRACTIn the Upper Cretaceous sequence of the Negev (southern Israel) the organic matter in phosphorites and cherts differs from that associated with oil shales in its higher content of humic substances and lower kerogen content, and in its more intensive microbial alteration. The n‐alkane distribution pattern of the oil shales, phosphorites and cherts indicates that marine biota, probably algae, are the main organic precursors of their organic matter. In some of the oil shales, however, some contribution of terrestrial organic matter is also evident. Similar high phytane/pristane ratios indicate that the organic matter in the oil shales as well as in the phosphorites and cherts accumulated under reducing conditions. The main differences in the organic matter composition are attributed to early diagenetic processes rather than to different biotic precursors or to late modifications due to temperature‐induced maturation. The depositional model suggested for the sequence involves upwelling conditions at the boundary between the deep Tethys and the shallow shelf, which induced high organic productivity deep into the inner shelf. Bottom water circulation enabled intensive microbial alteration of the organic matter, followed by a winnowing process leading to phosphorite formation. Since humification is considered an oxygen‐consuming reaction, these processes favoured the formation of oxygen‐enriched humic substances and the oxidation of humic substances already present. These humic substances are relatively resistant to further alteration and their conversion into kerogen is thus retarded. Subsequently, syndepositional tectonic activity resulted in the introduction of less saline water, restriction of bottom‐water circulation and the establishment of a density stratification in the water body. Consequently, aeration of the bottom layer and the sediments was inhibited, microbial alteration was reduced and later winnowing processes were prevented. Such conditions favoured the formation of kerogen directly, rather than through humic substances, and also favoured the preservation of most of the organic matter in the form of oil shale deposits instead of pho