The Lomonosov Ridge (LR) and Fram Strait (FR) represent prominent morphologic features in the Arctic Ocean. Their tectonic evolution control ocean circulation, sedimentation environment, glacial processes and ecosystem through time. We present findings of a 300 km long seismic transect from the Gakkel Deep through the southeastern Amundsen Basin (AB), and onto the LR. The data image an up to 3 km thick sedimentary sequence that can be subdivided into six major seismic units. The two lower units AB-1 and AB-2 consist of syn-rift sediments of Paleocene to early Eocene age likely eroded off the Barents-Kara and Laptev Sea shelves, and the subsiding LR. AB-2 includes the time interval of the “Azolla event,” which is regarded as an era of a warm Arctic Ocean punctuated by episodic incursions of fresh water. The connection to North Atlantic waters via the Fram Strait was not yet established, and anoxic conditions prevailed in the young, still isolated Eurasian Basin. Also, the LR still was above or close to sea level and posed an obstacle for water exchange between the Eurasian and Amerasian basins. The top of AB-2 onlaps the acoustic basement at magnetic anomaly C21o (∼47.3 Ma). Its contact with unit AB-3 above is marked by a striking loss in reflection amplitudes. This prominent interface can be traced through the AB, indicating widespread changes in tectonic and deposition conditions in the Arctic Ocean since the middle Eocene. For younger crust the depth of acoustic basement rises significantly, as well as the deformation of the surface. Both are probably linked to a reorganization of tectonic plates accompanied by a significant decrease in spreading rates. Units AB-3 and AB-4 indicate the accumulation of sediments between the middle Eocene and the earliest Miocene. Erosional, channel-like interruptions indicate these layers to reflect the stage when Fram Strait opened and continuously deepened. Incursions of water masses from the North Atlantic probably led to first bottom currents and produced erosion, slumping, and subsequent mixing of deposits. The upper units AB-5 to AB-6 show reflection characteristics and thicknesses similar all over the Arctic Ocean indicating that basin-wide pelagic sedimentation prevailed at least since late Oligocene. Drift bodies, sediment waves, and erosional structures indicate the onset of a modern ocean circulation system and bottom current activity in the early Miocene in the Amundsen Basin. At that time, the FR was developed widely, and also the LR no longer posed an obstacle between the Amerasia and Eurasia Basins. Lastly, unit AB-6 indicates pronounced variations in the sedimentary layers, and is associated with the onset of glacio-marine deposition since the Pliocene (5.3 Ma).