Abstract: An improved contact map reconstruction(COMAR) algorithm was introduced to reconstruct 3D structures from protein contact maps. After guessing a possible set of distances consistant with contact map, the proposed algorithm generates a random initial set of 3D coordinates, and then iteratively applies two local correction and perturbation techniques to the current set of coordinates. The results show that when the threshold of the contact map computation is increased, the reconstructed structure is more similar to the native structure. In addition, the RMSD computed by improved COMAR is lower than COMAR in the same case.