Recent reports indicate that the crystallization of clathrate hydrates occurs in multiple steps that involve amorphous intermediates and metastable clathrate crystals. The elucidation of the reaction coordinate for clathrate crystallization requires the use of order parameters able to identify the reactants, products, and intermediates in the crystallization pathway. Nevertheless, existing order parameters cannot distinguish between amorphous and crystalline clathrates or between different clathrate crystals. In this work, we present the first set of order parameters that discern between the sI and sII clathrate crystals, the amorphous clathrates, the blob of solvent-separated guests and the liquid solution. These order parameters can be used to monitor the advance of the crystallization and for the efficient implementation of methods to sample the rare clathrate nucleation events in molecular simulations. We illustrate the use of these order parameters in the analysis of the growth and the dissolution of clathrate crystals and the spontaneous nucleation and growth of clathrates under conditions of high supercooling. © 2011 American Institute of Physics.