We investigate the entanglement in a two-particle system with continuous degree of freedom constituted by trapped neutral atoms interacting via tunable dipole-dipole interaction. We describe the system in the quantum Wigner phase space representation. The atom entanglement is measured in terms of violation of the non separability condition or of some Bell inequalities. By an optimal control procedure, we design the control parameters that steer the system toward a maximally entangled state. We estimate the robustness of the control by considering the presence of an external source of noise weakly interacting with the atoms. •Optimal Control of an atomic gas in dipolar interaction.•Dynamical control of entanglement in interacting particles.•Optimal control applied to the Wigner phase space formalism.•Bell's inequalities and separability condition in continuous variable systems: phase space description.