The intertidal zone of the 34 islands that are the Boston Harbor Islands national park area encompasses over half of the total park area, thereby representing a significant natural resource. The purpose of this study was to inventory the intertidal zone by classifying and mapping all habitats and compiling species lists for major taxonomic groups. The Boston Harbor Intertidal Classification System was developed for mapping substrate and biotic assemblage types—a system specific to the local area, but capable of application throughout the Gulf of Maine. Intertidal habitats were mapped from GPS-based field delineations. Mixed coarse, consisting of rocks, boulders, cobbles, gravel, shell, and sand, was by far the most common substrate type; however, the islands were variable with a total of 13 discrete substrate types mapped, ranging from bedrock and boulders to mud. The outer islands (e.g., Outer and Little Brewster) were dominated by rocky substrate, while islands close to the mainland (e.g., Thompson, Slate) had high percentages of fine sediments. Of the 31 biotic assemblages mapped, Mytilus edulis (blue mussel) reef was the dominant assemblage on many of the middle and Hingham Bay islands, while the outer islands had assemblages common to the more exposed rocky substrates. The species inventory recorded 95 species of invertebrates, 70 marine algae, and 15 vascular plants. The information generated from this inventory will provide a foundation for natural resource management decisions, design of a long-term intertidal monitoring program, and identification of research needs.