Background. The Espiritu Santo archipelago is recognized for its high biodiversity as a national park. Studies carried out on soft-bottom mollusks are of the faunistic type, and little is known about the variations in their community structure. Objective. To know the composition and the spatial variation in the structure of the assemblages of soft-bottom mollusks of the archipelago and to describe the possible incidence of the type of substrate in their structuring. Methods. In the infralittoral zone, 66 sampling sites were distributed in nine locations. The mollusks were collected by autonomous diving using a 1 m-2metal frame and a nucleator to analyze of the sediment texture. The medium-grained sand substrate presented the highest distribution. The ecological indices of abundance, species richness (S), Shannon-Wiener diversity (H'), and Pielou evenness index (J') were estimated. Results. 23,743 individuals were quantified, belonging to 102 species distributed in three classes, 17 orders, 39 families, and 70 genera. The bivalves were represented by 48 species, 9 orders, 17 families, and 39 genera. The gastropods by 52 species, 7 orders, 21 families and 30 genera, and the scaphopods by 1 species. Significant differences were found between localities for species richness and diversity but not for species equity. Conclusions. Spatial variations were observed in the structure of the mollusks assemblages in the archipelago, which could be due to the combined effect of the sediment texture and the presence of mangroves existing in some locations. © 2022 Universidad Autonoma Metropolitana. All rights reserved.