We describe the deformation cohomology of a symplectic groupoid, and use it to study deformations via Moser path methods, proving a symplectic groupoid version of the Moser Theorem. Our construction uses the deformation cohomologies of Lie groupoids and of multiplicative forms, and we prove that in the symplectic case, deformation cohomology of both the underlying groupoid and of the symplectic groupoid have de Rham models in terms of differential forms. We use the de Rham model, which is intimately connected to the Bott-Shulman-Stasheff double complex, to compute deformation cohomology in several examples. We compute it for proper symplectic groupoids using vanishing results; alternatively, for groupoids satisfying homological 2-connectedness conditions we compute it using a simple spectral sequence. Finally, without making assumptions on the topology, we constructed a map relating differentiable and deformation cohomology of the underlying Lie groupoid of a symplectic groupoid, and related it to its Lie algebroid counterpart via van Est maps.
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