The vascular flora, natural communities, and natural community system on the Isles of Shoals in New Hampshire and Maine are described based on a combination of historical records dating back to 1614 and a comprehensive survey conducted in 2006. A total of 430 native or naturalized vascular plant taxa from 242 genera and 71 families have been documented on these nine maritime islands. The families best represented in the flora were Asteraceae (58 taxa), Poaceae (49 taxa), and Rosaceae (35 taxa); the largest genera were Carex (9 taxa), Juncus (8 taxa), Persicaria (7 taxa), and Solidago (7 taxa). Forty-two percent of the 430 plant taxa were non-native. Proportions among life forms were 86% herbs, 12% shrubs, and 2% trees. Plant richness for extant taxa totaled 333 and varied from 53 on White Island to 246 on Appledore. Fifteen plant taxa are rare in either New Hampshire or Maine. Fourteen natural communities, two human-disturbed cover types, and one natural community system were described from the nine islands. Eight of the 14 natural communities are extremely rare in New Hampshire; none of the communities are rare in Maine. Appledore, over twice the size of the next largest island, supported all 14 communities and both human-disturbed cover types. Seaveys, the second smallest island, supported just three communities. One natural community system was described, the maritime rocky shore, which characterizes all of the islands in the Isles of Shoals. Although not rare in Maine, this system in New Hampshire only occurs on these islands. Island size was significantly related to vascular plant richness and native plant richness but was somewhat less related to the richness of non-native plants.