From his earliest attempts at painting, Thayer was drawn to animals and nature, finding subjects in the forests and streams of New England. His careful observation of nature and thorough academic training in the laws of color and values led him to study how animals use natural camouflage to conceal themselves from predators. With his son Gerald, he published his theories as Concealing-Coloration in the Animal Kingdom (1909).

Thayer claimed that nature camouflaged animals by placing their darkest colors on their backs to counter the sunlight falling upon them, and their lightest colors closest to the dark ground. The fractured outlines and patterns, mimicking native habitats, would cause the animal to disappear when placed against the appropriate background.

The book drew considerable criticism, particularly from President Theodore Roosevelt, also an amateur naturalist. Roosevelt and others rejected Thayer's argument that the purpose of all animal coloration, no matter how conspicuous, was for the purpose of concealment. Some of Thayer's ideas were applied to camouflage during World War I.