Extensive study of modern Bahamian stromatolites has resulted in a comprehensive model for their formation. Modern Bahamian thrombolites—microbial deposits with a mottled, clotted fabric— have not, however, received the same degree of study. Current models link the Bahamian thrombolites with the presence of a mixed-bacterial-and-metaphyte benthic ecosystem, whereas stromatolite formation is linked with an almost exclusively bacterial benthic ecosystem. By focusing on the preserved fabrics of several specimens, including an entire column 1.5 meters tall, we have developed a new model for the genesis of the clotted, thrombolitic fabric. Our findings demonstrate that variations in the amount and style of penecontemporaneous diagenesis, rather than differences in surficial benthic ecosystems, are the predominate cause of the disparate carbonate fabrics present in the Bahamian microbialites examined. More specifically, the irregular, clotted fabric that characterizes the thrombolites is the result of remodeling a precursor fabric. This remodeling is caused by physical and metazoan disruption, penecontemporaneous micritization, secondary cementation, and localized carbonate dissolution. This new model of syndepositional remodeling of a laminated fabric to a well-cemented, clotted one may be applicable to some ancient thrombolites.