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The heats of formation of stable and metastable phases of the Nb–Si and Mo–Si systems were studied using density functional theory (DFT). The high-temperature behavior of the competing phases was studied by performing additional phonon calculations. Our theoretical results rationalize the major differences observed in the behavior of the Nb–Si and Mo–Si systems: Nb₃Si is only stable at temperatures above 2043K, whereas Mo₃Si is always stable; Nb₅Si₃ and MoSi₂ undergo phase changes at elevated temperatures, in contrast to Mo₅Si₃ and NbSi₂. These differences are qualitatively explained by including the vibrational entropy to the free energies within the harmonic approximation. In particular, the softer shear moduli of the Nb₅Si₃ and MoSi₂ β phases cause their stabilities over the α phases at elevated temperature.