<p>by James Matthew Ragle, Murugesan Pooranachithra, Guinevere E. Ashley, Emma Cadena, Batia Blank, Katelyn Kang, Cincy Chen, Aditree R. Bhowmick, Soraya H. Mercado, Tabatha E. Wells, John C. Clancy, Andrew D. Chisholm, Jordan D. Ward</p> Barrier epithelia are shielded from the external environment by their apical extracellular matrices (aECMs). The molecular complexity of aECMs has challenged understanding of their organization in vivo. To define the molecular architecture of a model aECM we generated a toolkit of 105 fluorescently tagged aECM components using gene editing in <i>C. elegans</i>, focusing on proteins secreted by the epidermis to form the collagen-rich cuticle. We developed efficient pipelines for modular protein tagging and rapid fluorophore swapping. Most tagged collagens were functional and exhibited exquisitely specific patterning across stages, cell types, and matrix substructures. We define multiple reference markers for key substructures including the little-understood cortical layer, as well as the helical crossed fiber arrays that function as a hydrostatic skeleton to maintain organismal shape. We further tagged 30 members of key aECM protein classes including proteases, protease inhibitors, and lipid transporters. Our standardized markers will allow dissection of the mechanistic basis of aECM spatiotemporal patterning in vivo.