Fifty years ago this June, patrons at the Stonewall Inn in New York resisted routine homophobic police harassment, sparking days of unrest and street rebellion and giving a public face to the emerging forces of gay liberation.

Surprisingly, however, the homophobia that sparked this uprising did not have deep roots in American history.

Although omnipresent in America by the Stonewall era, it was only around the 1930s that it started to emerge as a cogent cultural force, an explicit, widespread teaching that the world was divided into good heterosexuals and evil homosexuals (with, perhaps, a nasty, nebulous cloud formation called “bisexuality” located somewhere in between them).

As we celebrate this important milestone in the fight against homophobia, it is worth taking a moment to explore its roots. Anti-gay sentiments are usually traced to misogyny, fear of gender transgression, toxic masculinity and hidebound religious teachings. But one important factor regularly goes unacknowledged, curiously so, considering how often it comes up these days in other contexts: white supremacy.

In the early 20th century, leading white American intellectuals embraced the pseudoscience of eugenics, which held that human beings were the sum of inherited traits that could be read by looking at someone’s body.

The fullness of your lips, for instance, may indicate how decisive you were, or the swelling of breast tissue on a man, a condition called gynecomastia, may be a telltale sign of criminality. Eugenicists believed those moral and physical traits were inseparable, and that children inherited them in direct and simplistic ways, such as eye colour.

Therefore, the answer to all of society’s ills lay in controlling human reproduction: in breeding our way to a brighter future.

Eugenics was largely a response to the expanded political, social and geographical integration of black people in America, and those who practised it were interested in protecting and perfecting “the white race”.

These were men such as R.W. Shufeldt, a noted doctor with the US Army and a prolific author of eugenic treatises.

In his 1915 book America’s Greatest Problem: The Negro, Shufeldt argued that black women sought out white men because of their superior genes.

“It is the aim and highest ambition of the negresses to have children by white men,” he wrote, “for the reason that such children, by the superior intelligence coming from their white fathers, will command better positions when they grow up than the pure blacks, and in so doing will powerfully further the interests, political and otherwise, of the African population in this country.”

This was a follow-up to his 1907 book, The Negro: A Menace to American Civilisation, in which he wrote that a black man is “ready at any and at all times to do his share in debasing the blood of the white race in America”.

To protect whiteness, eugenicists such as Shufeldt fought for bans on interracial marriage, tighter medical control over marriage licences, increased power for the state to sterilise imprisoned people and increased regulations on prostitution, which they saw as a zone of possible race-mixing.

At the same time Shufeldt was writing about race, he was also researching a seemingly different topic: the defining of queerness, which he variously referred to as “passive pederasty”, “inversion”, “perversion” and “homosexuality”. Primarily, he studied men who had been arrested for soliciting other men, as well as people we would today call transgender women, who were often arrested under the charge of “masquerading in women’s clothes”.

As a eugenicist, Shufeldt didn’t believe that someone’s sexual nature could be changed because he believed it was hard-wired into the body — a more sinister ancestor to our modern idea of being “born this way”. But he did believe we could prevent queer people, in much the same way we could prevent racial miscegenation: by closely policing heterosexuality.

As he wrote in a 1905 paper titled The Medico-Legal Consideration of Perverts and Inverts, he believed that America “will continue to breed millions of sexual perverts and inverts, psychopathic types, just so long as any ignorant priest, justice of the peace or other party is permitted to give people permission to breed them.”

While this might seem far afield from his writings on race, it was really just the other side of the same eugenics coin: another effort to protect the white race through controlled breeding.

To Shufeldt, black people represented an external threat to whiteness, and queer people represented an internal one, the existence of black queer people seems never to have entered his mind. These were discrete issues, but they were both, at heart, about promoting white supremacy.

In the case of queer people, Shufeldt further recognised that the biggest problem facing eugenicists was the public’s lack of information. Until America understood that queer people existed, they couldn’t be enlisted in the effort to prevent breeding more of them.

Or as Shufeldt wrote in an impassioned plea for more sexological research, “how can we ever hope to improve the tissue of which our race is composed unless we are familiar with every cell now included in its composition?”

Shufeldt took a two-pronged approach to rectifying this ignorance. First, he studied queer people extensively, presenting them as pathetic human failures to be pitied, although, interestingly, not criminalised. He referred to one of his most frequent subjects as a “nervous, loquacious, foul-mouthed and foul-minded ‘fairy’,”, among other contemptuous descriptions.

Then, in order to popularise his findings, he fought against the obscenity laws that prevented the printing, mailing or sharing of publications that were deemed too erotic or sexual in nature. Writings by queer people were still suppressed, of course, but less so those about queer people, so long as they toed the line of the emerging medical and psychiatric consensus: that human sexuality was composed of two opposite orientations, which were inborn, unwavering and vastly unequal.

Thus, in an effort to protect whiteness, Shufeldt and his ilk cultivated a kind of medicalised homophobia, which simultaneously taught people that homosexuality existed and that they should despise it.

They were so successful in this endeavour that by the time of the Stonewall riots, even though eugenics had long since been discredited, their ideas had become the dominant way of understanding human sexuality.

Yet, in a bit of happy irony, Shufeldt’s fight for the freedom to discuss sexual matters, which he believed would help us to prevent queer children, and thereby save the white race, fundamentally enabled LGBTQ people to discuss their experiences and organise with one another.

Although we’re still fighting discriminatory local, state and federal policies, which have deep roots in white supremacy, eugenicists such as Shufeldt were thus ultimately hoisted by their own homophobic petards.

• Hugh Ryan is the author of When Brooklyn Was Queer