Henry Chandler Cowles (February 27, 1869 – September 12, 1939) was an American botanist and ecological pioneer.

He studied at the University of Chicago with the plant taxonomist John M. Coulter and the geologist Thomas Chrowder Chamberlin as main teachers.

The inspiration to these studies came from reading Plantesamfund by the Danish botanist and pioneer ecologist Eugen Warming.

Cowles Bog is located west of Mineral Springs Road in the Town of Dune Acres, Indiana.

Among Cowles's students who advanced American ecology were Victor E. Shelford, William Skinner Cooper, Paul B. Sears, George Damon Fuller, Walter P. Cottam, Arthur G. Vestal and May Theilgaard Watts.