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Transition-metal dichalcogenides of the pyrite–marcasite family are model systems of crystal chemistry. A few of these show polymorphism. The theoretical ground state of CoSe2 is marcasite, but the material is typically synthesized in the pyrite structure. Polymorphism has been observed in nanoparticles, and synthetic control of the polymorphs of CoSe2 has not been achieved. We have synthesized materials libraries of the Fe1–xCoxSe2 series by combining combinatorial deposition and ex-situ selenization. The approach allows us to efficiently explore substitution ranges and crystal structures that form for different synthesis conditions. We find that higher levels of Co content x within the marcasite structure are possible when synthesizing at low temperatures. At a synthesis temperature of only 250 °C, we have successfully synthesized marcasite CoSe2 as the majority phase. Density functional theory simulations reveal that the two isomorphs of CoSe2 are extremely close in energy and that the marcasite structure is the energetic ground state. Our experimental and theoretical data show that the marcasite structure is the equilibrium phase of Fe1–xCoxSe2 in the entire composition range.