Microbialite morphostratigraphy is a new tool for intrabasinal correlation using diverse microbialite structures (morphotypes). The recognition of the succession of morphotypes over constrained temporal intervals and broad areas is a function of the complex interactions that operate to create the structure. Because so many nonlinked variables (e.g., biotic, sedimentological, physicochemical) are involved, similar morphotypes do not reoccur over long temporal intervals. To demonstrate the technique, the upper Cambrian-lowermost Ordovician shelf strata of the Great Basin, United States, were correlated using both morphostratigraphy and standard lithostratigraphy. Six morphozones and one morphosubzone were recognized, as were four main lithologic successions. Because the boundaries between the morphozones and lithologic successions did not coincide, it is inferred that the characteristics of the various microbialite structures are not solely controlled by physical factors. The principles for establishing a morphostratigraphy outlined in this article allow for the potential to correlate along other ancient marine margins in both the same Cambrian and Ordovician interval, as well as any interval in the Phanerozoic in which diverse microbialite structures occur.