Quantum computation and simulation rely on long-lived qubits with controllable interactions. Trapped polar molecules have been proposed as a promising quantum computing platform, offering scalability and single-particle addressability while still leveraging inherent complexity and strong couplings of molecules1-5. Recent progress in the single quantum state preparation and coherence of the hyperfine-rotational states of individually trapped molecules allows them to serve as promising qubits6-11, with intermolecular dipolar interactions creating entanglement12,13. However, universal two-qubit gates have not been demonstrated with molecules. Here we harness intrinsic molecular resources to implement a two-qubit iSWAP gate using individually trapped X1Σ+ NaCs molecules. By allowing the molecules to interact for 664 μs at a distance of 1.9 μm, we create a maximally entangled Bell state with a fidelity of 94(3)% in trials in which both molecules are present. Using motion-rotation coupling, we measure residual excitation of the lowest few motional states along the axial trapping direction and find them to be the primary source of decoherence. Finally, we identify two non-interacting hyperfine states within the ground rotational level in which we encode a qubit. The interaction is toggled by transferring between interacting and non-interacting states to realize an iSWAP gate. We verify the gate performance by measuring its logical truth table.
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