The vegetation and flora of North and South Manitou Islands in northern Lake Michigan were surveyed during the summer of 1982 and the spring of 1983, the first comprehensive study of both islands. The vegetation associations were mapped and described, and a catalogue of 490 vascular plant species was compiled. A noticeable difference in forest structure and floristic composition between the islands was observed, largely due to an introduced deer herd on North Manitou. Twenty permanent plots were established on the islands to observe any future changes at selected sites. The island distributions of eight native species listed as threatened or of special concern by the State of Michigan were mapped and fragile habitats were identified. Recommendations concerning the resource management of these islands are proposed.