SUMMARY We investigate the upper mantle seismic structure beneath southern Madagascar and infer the imprint of geodynamic events since Madagascar’s break-up from Africa and India and earlier rifting episodes. Rayleigh and Love wave phase velocities along a profile across southern Madagascar were determined by application of the two-station method to teleseismic earthquake data. For shorter periods (<20 s), these data were supplemented by previously published dispersion curves determined from ambient noise correlation. First, tomographic models of the phase velocities were determined. In a second step, 1-D models of SV and SH wave velocities were inverted based on the dispersion curves extracted from the tomographic models. As the lithospheric mantle is represented by high velocities we identify the lithosphere–asthenosphere boundary by the strongest negative velocity gradient. Finally, the radial anisotropy (RA) is derived from the difference between the SV and SH velocity models. An additional constraint on the lithospheric thickness is provided by the presence of a negative conversion seen in S receiver functions, which results in comparable estimates under most of Madagascar. We infer a lithospheric thickness of 110−150 km beneath southern Madagascar, significantly thinner than beneath the mobile belts in East Africa (150−200 km), where the crust is of comparable age and which were located close to Madagascar in Gondwanaland. The lithospheric thickness is correlated with the geological domains. The thinnest lithosphere (∼110 km) is found beneath the Morondava basin. The pre-breakup Karoo failed rifting, the rifting and breakup of Gondwanaland have likely thinned the lithosphere there. The thickness of the lithosphere in the Proterozoic terranes (Androyen and Anosyen domains) ranges from 125 to 140 km, which is still ∼30 km thinner than in the Mozambique belt in Tanzania. The lithosphere is the thickest beneath Ikalamavony domain (Proterozoic) and the west part of the Antananarivo domain (Archean) with a thickness of ∼150 km. Below the eastern part of Archean domain the lithosphere thickness reduces to ∼130 km. The lithosphere below the entire profile is characterized by positive RA. The strongest RA is observed in the uppermost mantle beneath the Morondava basin (maximum value of ∼9 per cent), which is understandable from the strong stretching that the basin was exposed to during the Karoo and subsequent rifting episode. Anisotropy is still significantly positive below the Proterozoic (maximum value of ∼5 per cent) and Archean (maximum value of ∼6 per cent) domains, which may result from lithospheric extension during the Mesozoic and/or thereafter. In the asthenosphere, a positive RA is observed beneath the eastern part Morondava sedimentary basin and the Proterozoic domain, indicating a horizontal asthenospheric flow pattern. Negative RA is found beneath the Archean in the east, suggesting a small-scale asthenospheric upwelling, consistent with previous studies. Alternatively, the relatively high shear wave velocity in the asthenosphere in this region indicate that the negative RA could be associated to the Réunion mantle plume, at least beneath the volcanic formation, along the eastern coast.