The designation “thrombolite” was proposed by Aitken for “cryptalgal structures related to stromatolites, but lacking lamination and characterized by a macroscopic clotted fabric.” In that same paper, he referred to the characteristic mesostructural elements as clots. Since publication of that paper, there have been several attempts at redefinition that have further complicated our understanding of, and communication about, thrombolites.

A distinction must be made between the thrombolite column and the mesostructural clots (mesoclots) that comprise it. Poorly preserved thrombolite columns have only vague mesoclots recognizable, thus leading to confusion. This is particularly true if the columns, themselves, are complex and comprise larger thrombolite bioherms or biostromes. Mesoclots are generally polymorphic mm- to cm-sized objects whereas columns, which may also be polymorphic, are one to several orders of magnitude larger. In order for there to be clear communication among microbialite paleontologists and sedimentologists, a standard guideline for mega-, macro-, meso-, and microstructural studies of thrombolites should be followed.