The Late Jurassic was a period of major global carbon cycle perturbations with episodes of anoxia leading to regional accumulation of organic matter in sediments worldwide. The Tubiegatan section (SW Gissar Mountains, Uzbekistan) located in the Northern Tethys, shows atypical organic-rich limestone and marl deposits (up to 6% of total organic carbon) marked by pronounced negative excursions of δ13Ccarb (amplitude of ca. 12‰) and δ13Corg (amplitude of ca. 4‰) recorded during the Middle Oxfordian (Transversarium Zone). A transdisciplinary approach including sedimentology, palynofacies characterization, mineralogy, organic and inorganic geochemistry was carried out to elucidate the origin of these organic-rich deposits. Highest TOC are measured in nodular limestones, and lowest δ13Ccarb values in thinly laminated facies consisting in alternances of infra-millimeter-thick organic and carbonate laminae. In the latter, the presence of organic-carbonate peloids and of possible remnants of exopolymeric substances associated with clay indicate that these structures are probably mineralized laminated benthic microbial mats (i.e., stromatolites). Rock-Eval pyrolysis coupled to palynofacies analyses point to a dominant altered marine organic matter of probable algal/microbial origin, with subordinate continental phytoclasts inputs in the upper part of the organic-rich interval. Trace elements (U/Th, V/Cr and Mo/Al ratios) indicate two anoxic episodes coinciding with the highest TOC, punctuated by dysoxic periods. Such O2-depleted conditions have allowed the preservation and probably the development of anaerobic microbial communities in the microbial mats. In these latter, sulfate reduction probably had a significant contribution to the production of carbonates, which would explain the precipitation of pyrite and the relatively low δ13Ccarb values. The progressive decrease then disappearance of kaolinite from the base of the organic-rich interval, is interpreted as a progressive aridification of the Amu Darya Basin during the Transversarium Zone, culminating with the progradation of a large-scale gypsum sabkha overlying the organic deposits. Overall, the organic-rich deposits could record the onset of the disconnection of the Amu Darya Basin from the open sea to the south, induced by compression and subsequent uplifts in the Afghan and Central Iranian blocks. The elevated evaporation, coupled with the presence of hydrological barriers (such as coral reefs) could have led to the formation of local to regional anoxic conditions in the Amu Darya Basin. Similar microbial organic accumulations are recently known throughout the Tethys (e.g., Arabian Plate, Western Europe) and from other oceans (e.g., Central Atlantic, Pacific) during the Late Jurassic, suggesting common controlling factors. The increase of organic matter storage worldwide coupled with potential methane release could have in turn induced major perturbations of the carbon cycle during the Oxfordian-Kimmeridgian interval. The relatively shallow anoxia model proposed in this study contrasts with the well-known organic carbon-rich pelagic models proposed for the Jurassic anoxia (e.g., Toarcian, Kimmeridgian) and Cretaceous OAEs.