Madagascar is a large producer of gem corundum recovered from continental basaltic fields. The main mining areas are sapphire-bearing palaeoplacer deposits such as Ambondromifehy and Nosy Be in Antsiranana Province, northern Madagascar; Soamiakatra–Mandrosohasina in Antananarivo Province, central Madagascar; and Vatomandry district in Toamasina Province, eastern Madagascar. In Antananarivo Province, Soamiakatra is a primary deposit where ruby is found in metagabbro and pyroxenite xenoliths, brought-up to the upper crust by the Ankaratra volcanics. Petrographic studies indicate two different conditions of ruby formation, at the boundary of the eclogite domain (T ∼ 1100 °C, P ∼ 20 kb) and granulite facies (T ∼ 1100 °C, P < 15 kb). In contrast, most of the sapphires in placer and paleoplacer have two origins: (i) differentiation of alkaline magma in chambers at the lower continental crust–mantle boundary (90% of the sapphires). They are related to syenite and anorthoclasite xenoliths in the basalts. These alkali-basalt hosts are linked with asthenosphere upwelling and E–W and N–S lithosphere thinning during Oligocene–Quaternary times. Zircons associated with the sapphires from Mandrosohasina and Ambatomainty sapphire deposits gave U–Pb ages at 7 Ma. The sapphires have low δ18O values of 4.1 ± 0.4‰ (n = 8), within the range of sapphire in syenitic rocks. Chemical composition and mineral inclusions in sapphires, such as columbite-(Fe), tantalite-(Mn), pyrochlore group, samarksite group, uraninite and anorthoclase confirm their syenitic origin. (ii) metamorphic xenocrysts (10%) brought up by the same magma. Oxygen isotopic compositions of rubies from placer deposits, δ18O = 3.1 ± 1.1‰ (n = 6) are typical of ruby in mafic and ultramafic rocks and ‘plumasite’ in mafic rocks (1.25 < δ18O < 7.5‰, n = 35). In Toamasina Province, the sapphires of Vatomandry are mainly of metamorphic origin (∼85%) and their δ18O = 4.1 ± 0.4‰ (n = 9) are low and overlaps the range defined for metasomatic sapphires linked to ‘plumasites’ and biotite schists in shear zones; ∼15% of the sapphires are magmatic in origin with a low δ18O-isotopic range in the sapphire-bearing syenites field. In Antsiranana Province, there are no rubies and sapphires are either magmatic (∼40%) or metamorphic (∼60%) in origin. The δ18O = 4.5 ± 0.5‰ (n = 11) values are similar to the mean δ18O of sapphires from other two Provinces. Two U/Pb ages on zircons gave two contrasted ages at respectively 40.6 Ma for Ambondromifehy and 0.7 Ma for Nosy Be sapphire deposits. The characteristics of the corundum, their isotopic compositions as well as their ages demonstrate the existence of two distinct sources of corundum associated with alkali-basalts in Madagascar. On one hand, the rubies associated with metagabbros and garnet-bearing pyroxenites are linked to mafic and ultramafic complexes of eclogite facies at the boundary between lower crust and upper mantle, retrograded to granulite facies during the Pan-African event. On the other hand, the sapphires brought up during the Eocene to Quaternary are interpreted to be either magmatic and coeval with a volcanic event involving differentiated alkaline magma, or metamorphic and extracted from the pre-existing Precambrian basement during the extrusion of the magma.