The national lakeshore provides habitat for 1,130 native vascular plants, including the federally threatened Pitcher's thistle. The lakeshore is home to populations of 30% of the state of Indiana's listed rare, threatened, endangered, and special concern plant species. Shaped by glacial events and changing climates, the dunes landscape contains disjunct flora representative of eastern deciduous forests, boreal forest remnants, and species with Atlantic coast affinities. In addition, the national lakeshore is part of the upper- and eastern-most limits of the tallgrass prairie peninsula and supports high quality remnants of this ever-diminishing vegetation type.
The presence of many unique dune and wetland plant community types has lead to a long history of botanical exploration and research. Lands within the national lakeshore have been called the birthplace of American ecology as a result of early work on plant succession performed by Dr. Henry Cowles over 100 years ago. Investigations related to several areas of plant ecology continue today and are viewed as essential to preserving the dynamic ecosystems of the Indiana Dunes.