At Wesleyan University, Trinkaus majored in biology. In his memoirs, he recalled feeling that his high school had not prepared him well for the work required by college students, and that his freshman year in 1936 started off on a bad note, during which he failed his first math exam and got a D on an English assignment. During that first year in college, Trinkaus found a job making charts for biology classes for Professor Hubert B. Goodrich, who later became his research mentor at Wesleyan. His undergraduate research began with a study on the effect of ultraviolet light on the skin pigmentation of Carassius auratus, the common goldfish. Trinkaus remembered his first try at scientific research as a good learning experience, as he learned how to handle biological specimens carefully, how to observe and record any changes in the treatments at regular time intervals, and how to read the literature on his research topic to acquire the appropriate scientific context and background. This work led to Trinkaus’s first publication in the Biological Bulletin, titled “The differential effect of radiations on Mendelian phenotypes of the goldfish,” in 1939. The next research project assigned to Trinkaus was also related to the developmental physiology of the pigmentation patterns in fish; this time, on the guppy, or Poecilia reticulate. This research was the basis for Trinkaus’s undergraduate honours project, in which he described the genetics of a new variety of this species of fish. Trinkaus graduated from Wesleyan in 1940 with high distinction and published his work on P. reticulate in Genetics in 1944.