Strong environmental gradients and varied land-use practices have generated a mosaic of habitats harboring distinct plant communities on islands on the coast of Maine. Botanical studies of Maine's islands, however, are generally limited in number and scope. Baseline studies of Maine's islands are necessary for assessing vegetation dynamics and changes in habitat conditions in relation to environmental impacts imposed by climate change, rising sea levels, invasive species, pests and pathogens, introduced herbivores, and human disturbance. We conducted a survey of the vascular plants and soils of forest, field, and ocean-side communities of Great Duck and Little Duck Islands, ME. These islands differ in environmental and land-use features, and in particular the presence of mammalian herbivores; Great Duck Island has had over a century of continuous mammalian herbivory while Little Duck Island has been largely free of mammalian herbivores over the last 100 years. We recorded 235 vascular plant species in 61 families on the Duck Islands, 106 of which were common to both islands. The composition, abundances, and diversity of plant species substantially differed within similar plant communities between the islands. These differences were particularly evident in the forest communities where Little Duck Island had significantly greater sapling regeneration and a more recent peak in tree recruitment. Soil properties also significantly differed between these islands, with a higher pH in all three communities and higher P, Ca, and K in field, forest, and ocean-side communities, respectively, on Little Duck Island, and higher soluble salts in forest and ocean-side communities of Great Duck Island. Together, our findings suggest that soil characteristics and the dominance and regeneration of vascular plant species can differ substantially even between adjacent islands with otherwise similar geologic characteristics and glacial history, and that mammalian herbivory along with other ecological factors may be important drivers of these differences.