This paper focuses on coordination of multi-agent systems with agents having holonomic nonlinear dynamics and uncertain system parameters. An indirect adaptive control scheme composed of a parameter estimator and a feedback-linearization based control law is designed based on the certainty equivalence principle. (i) Simple linear and (ii) sliding mode control structures are used in the outer control loop. The controllers successfully satisfy the objectives of formation maintenance and trajectory tracking. Simulation results for a sample two-dimensional formation are presented, demonstrating the performance of the proposed control scheme. © 2013 IEEE.