Carothers stayed on as assistant professor until 1936, though she also had an overlapping appointment as an independent investigator for the Marine Biological Laboratory, which lasted from 1920 until 1941.

[2] While studying and teaching at the University of Pennsylvania, Carothers traveled to the southern and southwestern regions of the United States on research expeditions, held in 1915 and 1919.

During her time at the University of Iowa, she completed her most important work, in the field of genetics and cytology, using grasshopper embryos to study the independent assortment of heteromorphic homologous chromosomes.

[2] This was the first physical evidence that homologous chromosomes separated independently during meiosis, which is one source of genetic variation in sexually-reproducing organisms.

She received a starred entry for her work on grasshopper embryos in the fourth edition of American Men of Science, published in 1927, a rare and significant award for a female scientist at the time.