From 2001 to 2003, 32 islands in the Boston Harbor Islands national park area were surveyed and inventoried for vascular plant species and plant communities. To date, 521 species in 99 plant families have been identified on these islands. A total of 229 species (44%) are exotic plants. On many islands, non-native plants account for 50% or more of the total flora. The islands with the largest number of plant species are: Worlds End (301), Peddocks (225), and Thompson (211). Duration and type of human uses are influential factors determining the present condition of the flora in the park. Seven rare plant taxa listed as endangered, threatened, special concern, or watch-list by the Massachusetts Natural Heritage and Endangered Species Program were documented on the Harbor Islands in this survey.

Upland vegetation communities on 18 islands have been surveyed, classified, and mapped. Plant communities found on the Harbor Islands include native and non-native forests and woodlands, maritime shrub communities, old fields, beach strand communities, maritime cliff communities, and dune systems.