His ideas were largely dismissed during his working life, leading him to move into plant taxonomy, but found favour late in the twentieth century.

Building on Henry C. Cowles's landmark research at the Indiana Dunes and some of the ideas of his mentor Charles Bessey at the University of Nebraska, Clements had developed a theory of plant succession in which vegetation could be explained by reference to an ideal sequence of development called a sere.

(What units should be used in the analysis of vegetation was a widely disputed issue in early twentieth-century ecology.)

As an alternative to describing vegetation in terms of associations, Gleason offered "the Individualistic concept of ecology," in which "the phenomena of vegetation depend completely upon the phenomena of the individual" species (1917), and plant associations are less structured than he thought Clements's theory maintained.

[3] Their elder son, Henry Allan Gleason Jr (1917–2007), was a linguist and Professor Emeritus at the University of Toronto.