A consensus is now emerging that the structure of organic macromolecules will determine their function in aquatic systems. Transmission electron microscopy (TEM) is a widely used technique to study the morphology of biomolecules that, under the proper conditions, allows for accurate determination of the shapes and horizontal dimensions of macromolecules. Atomic force microscopy (AFM) is a newe: technique that has better overall resolution, particularly on the vertical scale. Although careful controls must be in place for both techniques to avoid the introduction of artifacts, they are highly complementary techniques for the study of natural colloids and can, when used together, reveal complementary information about the relative abundance and structures of aquatic macromolecules and colloids. Although AFM techniques have not previously been applied to the study of oceanic macromolecules and colloids, TEM has been used, albeit often under nonoptimal staining and embedding conditions. In this study, colloid samples from the Gulf of Mexico and Middle Atlantic Bight of nominal sizes 1–200 nm were collected by cross-flow ultrafiltration, diafiltered, and freeze-dried. Rehydrated colloids were analyzed in parallel by AFM and TEM using standardized techniques. Results from estuarine-, surface-, and deep-water samples show that an important fraction of colloidal organic matter (COM) consists of fibrillar material, which is rich in polysaccharides and “fresher” (i.e., has a younger radiocarbon age) than the bulk COM. This result is important because COM makes up 30–70% of oceanic and estuarine nominally “dissolved” organic matter. Other microparticles appear to be quasi-spherical, often attached to the fibrils like pearls. In the surface waters of the Gulf of Mexico, Middle Atlantic Bight, and Trinity River, fibrils with diameters of l–3 nm and lengths of 100–2,000 nm were predominant. Although fibrils were also observed in samples from the benthic nepheloid layer in the Gulf of Mexico (1,600 m) and Middle Atlantic Bight (2,600 m), a much greater heterogeneity of colloid and macromolecule shapes and sizes was observed in these deeper waters.