After being turned down for a scholarship to go to Trinidad as a farmer, Cyril was induced in 1923 by one of his professors to apply for a scholarship at the John Innes Horticultural Institution in Merton. He wrote at once to its director, William Bateson, famous for having introduced the word "genetics" into biology. His application was unsuccessful, but he wrangled a temporary post as an unpaid technician. It was an interesting time for the Innes. Bateson had spent the last two decades fighting against the notion that chromosomes were the seat of what he had been calling "heredity factors" and had only very recently capitulated. He had just hired a cytologist, Frank Newton, who now began to take Cyril under his wing. Darlington published his first scientific paper, on the tetraploidy of the sour cherry, and he was hired as a permanent employee.

Shortly after, both of his mentors, Bateson and Newton, died within a year of each other and J.B.S. Haldane came to the Innes. Although neither an experimentalist nor cytologist, Haldane formed a close friendship with Darlington, whose self - confidence grew. He began to make significant contributions to the understanding of the relationship of genetic crossing - over and the microscopically observed events that the chromosome passed through during meiosis. In 1931 he began writing the book that would establish his reputation, Recent Advances in Cytology. It was published in 1932, and created a firestorm of controversy at first, then nearly universal acceptance as a work of the first rank. He showed that the mechanisms of evolution that acted at the level of the chromosome created possibilities far richer than the simple mutations and deletions that affect single genes.

His now remarkable determination and achievement saw him become Director of the cytology department in 1937 and became director of the Innes two years later, just 15 years after his arrival as an unpaid volunteer. He was elected a Fellow of the Royal Society on 20 March 1941. A few months after that, he was awarded the prestigious Darwin Medal. He was elected president of the Genetical Society. In 1947 he co-founded with Ronald Fisher the highly successful journal Heredity: An International Journal of Genetics, as a response to J.B.S. Haldane joining the Communist party and "taking the Journal of Genetics with him".

He left the Innes in 1953 and accepted the Sherardian chair of botany at Oxford University. He developed a keen interest in the Botanic Garden, going on to establish the 'Genetic Garden'. He was also involved in extending the teaching of science, especially genetics, in the university. He voiced strong support for hereditarians in an increasingly hostile academic environment. In 1972 he, along with 50 other prominent scientists signed "Resolution on Scientific Freedom Regarding Human Behavior and Heredity" in which a genetic approach to understanding the behavior of man was strongly defended. He staunchly defended his colleague in the fight against Lysenkoism, John Baker, who published the controversial book "Race" in 1974. Races are, according to Baker (and Darlington), breeding populations with demarcations drawn at whatever level of detail is required for the problem at hand. Asked by a reporter for the Sunday times whether or not he was a racist, Darlington replied: "Well, I'm regarded as one by everyone except the Jews, who are racist, and who utterly agree with my views."

Darlington retired from his official position at the University in 1971, but remained in the university, tirelessly writing and publishing his work. He died in Oxford in 1981. He had five children, two of whom committed suicide.

In his later years, Darlington increased his participation in the public debate about the role of science in society, and especially, its interaction with politics and government. He published, beginning in 1948, very strong condemnations of the events in the Soviet Union, which had denounced Mendelian genetics and officially outlawed its practice in favor of Lysenkoism. Some genetics institutes were destroyed, and prominent geneticists were purged or murdered. These events caused an upheaval among the leaders of genetics in the west, many of whom were leftist, socialists or even communist sympathizers and Marxists. This caused a break between Haldane and Darlington, who was intransigent in his anti-authoritarian views.

Darlington developed a strong interest in the application of genetic insights to the understanding of human history. He believed that not only were there differences in the character and culture between individuals, but that these differences also exist between races. Understanding of these differences in scientific terms was not only interesting in its own right, but was crucial to the development of a civil society.

The nature of his views on race is well illustrated by his essay in Human Variation: The Biopsychology of Age, Race, and Sex (Academic Press 1978). Darlington writes that "as slaves," Africans "improved in health and increased in numbers." The environment was "more favorable than anything they had experienced in Africa." According to Darlington, emancipation resulted in the withdrawal of "discipline" and "protection" resulting in social problems such as unemployment "drugs, gambling and prostitution." Darlington concluded: "The intellectually well endowed races, classes, and societies have a moral responsibility for the problems of race mixture, of immigration and exploitation, that have arisen from their exercise of economic and political power. They may hope to escape from these responsibilities by claiming an intellectual and, therefore, moral equality between all races, classes, and societies. But the chapters of this book, step by step, deprive them of the scientific and historical evidence that might support such a comfortable illusion."

Darlington was opposed to the UNESCO Statement of Race. He agreed with Darwin's classical view: "The races differ also in constitution, in acclimatization, and in liability to certain diseases. Their mental characteristics are likewise very distinct; chiefly as it would appear in their emotional, but partly in their intellectual, faculties." Contrary to the UNESCO statement. Darlington thought that there might be a biological justification to prohibit interracial marriages "if intermarriage were not contrary to the habits of all stable communities and therefore in no need of discouragement". He refused to sign the revised 1951 statement which conceded that racial differences in intelligence possibly existed. Darlington's dissenting commentary was printed with the statement.

Over the course of twenty five years, from 1953 - 1978, Darlington completed his trilogy on Man: Genetics and Man (1953), The Evolution of Man and Society (1969) and finally The Little Universe of Man (1978). In these he tried to show how the history of man can be at least partially analyzed in terms of genetic laws, breeding patterns, founder effects and Darwinian evolution. Darlington's views were an unusual endorsement of the complementary virtues of inbreeding, as well as of outbreeding.

Darlington's personality was one of a remarkable combination of anti-authoritarianism, non-conformism, and scientific rationalism. He was as courageous in fighting the evils of Lysenkoism, as he was in combating the emerging academic orthodoxy on the nature of race. His method was not that of a simple bench scientist, but ranged far into the hinterlands of human existence. His penchant for speculation and theorizing was his strongest tool for arriving at new insights and truth. He said "...I have never proved anything. I do not count on doing so...What I do count on is to assemble such evidences and arguments as will make those who disagree with me feel more and more uncomfortable."