The genesis of several groups of pyroxenite xenoliths from Miocene picrobasalt of the Vitim volcanic field are considered on the basis of petrology and mineral chemical data, including trace element analyses of minerals by ion probe. The pyroxenites and related xenoliths can be classified into three groups consisting of 10 sets of xenoliths: Group I (Cr-diopside series) is made up by three subdivisions; (Ia) common Cr-diopside garnet and spinel websterites, (Ib) Al-poor Cr-diopside websterites, (Ic) modally metasomatized Cr-diopside lherzolites. Group II (Al-augite series) consists of four further xenolith types; (IIa) Cr-rich and (IIb) Cr-poor megacrystic pyroxenite assemblages, (IIc) Al-rich garnet clinopyroxenites, and (IId) amphibole and/or phlogopite-bearing rocks and associated orthopyroxenites. Group III consists of xenoliths all characterized by Ca-rich clinopyroxene (garnet clinopyroxenite and gabbros, garnet granulites and spinel websterites) thought to have a similar depth of origin near the crust–mantle boundary. Trace element data and textural criteria allow the distinction of three melt types operating in the mantle: (1) Cr-rich melt migrating along small fractures and forming Cr-diopside pyroxenite veins as the result of percolation fractionation; (2) picrobasaltic to alkaline basaltic melt fractionating in large hydraulic fractures or magma chambers and producing host volcanics, clinopyroxene megacrysts and megacrystic pyroxenites (Groups IIa–IIb); and (3) high field strength element (HFSE)-enriched smaller volume melts, which formed the hydrous mineral-bearing xenoliths of Groups I and II (Ic and IId). The megacrystic pyroxenites (IIa–IIb) were crystallized in magma chambers or large fractures at various depths during multistage polybaric fractionation. The high-temperature Cr-rich websterites (Group IIa) correspond to the deepest level at near 30 kbar. The garnet websterites and megacrystic clinopyroxenites crystallized at intermediate levels, whereas the most differentiated megacrystic clinopyroxenites with ilmenite and phlogopite inclusions are from the shallowest levels at 15–11 kbar. The HFSE-rich melt resulted in amphibole- and phlogopite-rich assemblages crystallized in veins and interstitially in peridotites, and the development of ilmenite–phlogopite-bearing orthopyroxenites in a reaction zone between these. Pyroxenites of Groups I and II represent samples of an intensely veined sub-Vitim lithosphere: the preservation of textural and chemical disequilibrium indicates that the enrichment immediately preceded xenolith sampling and is related to the upward and outward migration of the asthenosphere–lithosphere boundary beneath the developing Baikal Rift. The formation of lower pressure xenoliths (Group III) is related to both of the first two melt types mentioned above. Spinel websterites of Group III are genetically related to the Group Ia melt crystallized near the crust–mantle boundary, and the mafic garnet granulites of Group III to intermediate fractionation products (gabbro-norites) of similar melts. Garnet gabbros are associated with the most fractionated megacrystic pyroxenites.