Eccentric and opinionated, Thayer grew more so as he aged, and his family's manner of living reflected his strong beliefs: the Thayers typically slept outdoors year-round in order to enjoy the benefits of fresh air, and the three children were never enrolled in a school. The younger two, Gerald and Gladys, shared their father's enthusiasms, and became painters. In 1898, Thayer visited St Ives, Cornwall and, with an introductory letter from C. Hart Merrian, the Chief of the US Biological Survey in Washington, D.C., applied to the lord of the Manor of St Ives and Treloyhan, Henry Arthur Mornington Wellesley, the 3rd Earl Cowley, for permission to collect specimens of birds from the cliffs at St Ives. During this latter part of his life, among Thayer's neighbors was George de Forest Brush, with whom (when they were not quarreling) he collaborated on camouflage.
Thayer first became involved in military camouflage in 1898, during the Spanish–American War, when he and his friend George de Forest Brush proposed the use of protective coloration on American ships, using countershading. The two artists did obtain a patent for their idea in 1902, titled "Process of Treating the Outsides of Ships, etc., for Making Them Less Visible", in which their method is described as having been modeled on the coloration of a seagull.