Dolomite, an ordered Ca-Mg-carbonate mineral, is abundant in the sedimentary record but found only rarely found in Holocene and modern marine settings. Instead, protodolomite, a partially ordered Ca-Mg-carbonate with a composition close to ideal dolomite, and disordered dolomite occur in specific modern sedimentary settings. In this study, the protodolomite in a late Holocene stromatolite collected from Manito Lake, Saskatchewan, Canada, was examined using X-ray diffraction (XRD), scanning electron microscopy (SEM), transmission electron microscopy (TEM), and Z-contrast imaging from scanning-transmission electron microscopy (STEM). The protodolomite is characterized by nano-domains exhibiting a weak to moderate degree of Ca-Mg ordering based on attenuated and diffuse “b” reflections in selected-area diffraction patterns. The stromatolite also contains disordered dolomite that lack “b” reflections. Using Z-contrast images and image simulations, a quantitative approach was developed to calculate and constrain the ordering state of protodolomite, a parameter that is generally difficult to determine. With ordering contour lines constructed from this study, the ordering state of a weakly ordered dolomite can be quantified based on its d104 value and composition.