We present model of the structure and development of the entire lithosphere beneath the western Eger Rift (ER). Its crustal architecture and paths of volcanic products are closely related to sutures/boundaries of uppermost mantle domains distinguished by different orientations of olivine fabric, derived from 3-D analysis of seismic anisotropy. Three different fabrics of the mantle lithosphere belong to the Saxothuringian (ST), Tepla-Barrandian (TB) and Moldanubian (MD) microplates assembled during the Variscan orogeny. Dipping fossil (pre-assembly) olivine orientations, consistent within each unit, do not support any voluminous mantle delamination. The variable rift structure and morphology depend on the character of the pre-rift suture between the northern ST unit and the TB/MD units in the southern rift flank. The proper rift with typical graben morphology has developed above the steep lithosphere-scale suture between the ST and TB units. This subduction-related boundary originated from the closure of the ST Ocean. Parts of the crust and mantle lithosphere were dragged there into asthenospheric depths and then rapidly uplifted. The suture is marked by abrupt change in the mantle fabric and sharp gradients in regional gravity field and in metamorphic grade. The secular TB-side-down normal movement is reflected in deep sedimentary basins, which developed since the Carboniferous to Cenozoic and in topography. The graben morphology of the ER terminates above the “triple junction” of the ST, TB and MD mantle lithospheres. The junction is characterized by offsets of surface boundaries of the tectonic units from their mantle counterparts indicating a detachment of the rigid upper crust from the mantle lithosphere. The southwest continuation of the rift features in Bavaria is expressed in occurrences of Cenozoic sediments and volcanics above an inclined broad transition zone between the ST and MD lithospheres. Schematic scenario of evolution of the region consists mainly of a subduction of the ST lithosphere to depths around 140 km, exhumation of HP-HT rocks and the post-tectonic granitoid plutonism.