We study the quark-antiquark interaction in the large-N limit of the superconformal field theory on D3-branes at a Calabi-Yau conical singularity. We compute the Wilson loop in the AdS₅ × T¹¹ supergravity background for the SU(2N) × SU(2N) theory. We also calculate the Wilson loop for the Higgs phase where the gauge group is broken to SU(N) × SU(N) × SU_D(N). This corresponds to a two center configuration with some of the branes at the singularity and the rest of them at a smooth point. The calculation exhibits the expected Coulomb dependence for the interaction. The angular distribution of the BPS states is different than the one for a spherical horizon.