The Triassic?Jurassic (Tr?J) boundary marks a major extinction event, which (~200 Ma) resulted in global extinctions of fauna and flora both in the marine and terrestrial realms. There prevail great challenges in determining the exact location of the terrestrial Tr?J boundary, because of endemism of taxa and the scarcity of fossils in terrestrial settings leading to difficulties in linking marine and terrestrial sedimentary successions. Investigation based on palynology and bivalves has been carried out over a 1113 m thick section, which is subdivided into 132 beds, along the Haojiagou valley on the southern margin of the Junggar Basin of the northern Xinjiang, northwestern China. The terrestrial Lower Jurassic is conformably resting on the Upper Triassic strata. The Upper Triassic covers the Huangshanjie Formation overlaid by the Haojiagou Formation, while the Lower Jurassic comprises the Badaowan Formation followed by the Sangonghe Formation. Fifty six pollen and spore taxa and one algal taxon were identified from the sediments. Based on the key-species and abundance of spores and pollen, three zones were erected: the Late Triassic (Rhaetian) Aratrisporites?Alisporites Assemblage, the Early Jurassic (Hettangian) Perinopollenites?Pinuspollenites Assemblage, and the Sinemurian Perinopollenites?Cycadopites Assemblage. The Tr?J boundary is placed between bed 44 and 45 coincident with the boundary between the Haojiagou and Badaowan formations. Beds with Ferganoconcha (?), Unio?Ferganoconcha and Waagenoperna?Yananoconcha bivalve assemblages are recognized. The Ferganoconcha (?) bed is limited to the upper Haojiagou Formation, Unio?Ferganoconcha and Waagenoperna?Yananoconcha assemblages are present in the middle and upper members of the Badaowan Formation. The sedimentary succession is interpreted as terrestrial with two mainly lake deposit intervals within Haojiagou and Badaowan formations, yielding fresh water algae and bivalves. However, the presence of brackish water algae Tasmanites and the marine?littoral facies bivalve Waagenoperna from the Badaowan Formation indicate that the Junggar Basin was influenced by sea water caused by transgressions from the northern Tethys, during the Sinemurian.