We study Wilson loops in the three-dimensional N=6 supersymmetric Chern-Simons theory recently constructed by Aharony, Bergman, Jafferis and Maldacena, that is conjectured to be dual to type IIA string theory on AdS_4 x CP^3. We construct loop operators in the Chern-Simons theory which preserve 1/6 of the supercharges and calculate their expectation value up to 2-loop order at weak coupling. The expectation value at strong coupling is found by constructing the string theory duals of these operators. For low dimensional representations these are fundamental strings, for high dimensional representations these are D2-branes and D6-branes. In support of this identification we demonstrate that these string theory solutions match the symmetries, charges and the preserved supersymmetries of their Chern-Simons theory counterparts.