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 Tubegatan 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 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 study, mineralogy, organic and inorganic geochemistry was carried out to elucidate the origin of these organic-rich deposits. Higher TOC and lowest δ13Ccarb values are measured in nodular limestones characterized by thinly laminated facies consisting in alternances of infra-millimeter-thick organic and carbonate laminae. The presence of organic-carbonate peloids and of possible remnants of exopolymeric substances associated with clay indicate that these structures are probably mineralized benthic microbial mats (i.e., stromatolites). Rock-Eval pyrolysis coupled to palynofacies analyses point to a dominant likely 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 periodes. Such O2-depleted conditions have allowed the preservation and probably the development of anaerobic microbial communities in the microbial mats. In these latter, the precipitation of carbonates likely formed during sulfate reduction and anaerobic oxidation of methane, which would explain the abundance of pyrite and the very 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 in the Upper Jurassic. 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 (possibly coral reefs) could have led to the formation of local anoxic environments. Similar organic microbial accumulations are recorded 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 relatively shallow anoxia model proposed in this study contrasts with the well-known organic carbon-rich pelagic models proposed for the Jurassic (Toarcian, Kimmeridgian) and Cretaceous OAEs.