Long coherence times are key to the performance of quantum bits (qubits). Here, we experimentally and theoretically show that the Hahn-echo coherence time (T2) of electron spins associated with divacancy defects in 4H-SiC reaches 1.3 ms, one of the longest T2 times of an electron spin in a naturally isotopic crystal. Using a first-principles microscopic quantum-bath model, we find that two factors determine the unusually robust coherence. First, in the presence of moderate magnetic fields (300 G and above), the 29Si and 13C paramagnetic nuclear spin baths are decoupled. In addition, because SiC is a binary crystal, homo-nuclear spin pairs are both diluted and forbidden from forming strongly coupled, nearest-neighbor spin pairs. Longer neighbor distances result in fewer nuclear spin flip-flops, a less fluctuating intra-crystalline magnetic environment, and thus a longer T2 time. Our results point to polyatomic crystals as promising hosts for coherent qubits in the solid state.