When Stephane Castel first met with a group of Māori people and other Pacific Islanders in New Zealand to talk about his drug company’s plans for genetic research, locals worried he might be seeking to profit from the genes of community members without much thought to them.

Instead, Dr. Castel and his colleagues explained, they were aiming to strike an unconventional bargain: In exchange for entrusting them with their genetic heritage, participating communities would receive a share of the company’s revenues. Dr. Castel also vowed not to patent any genes — as many other companies had done — but rather the drugs his company developed from the partnership.

“A lot of people told us this was a crazy idea, and it wouldn’t work,” Dr. Castel said. But five years after that first conversation during an Indigenous health research conference in March 2019, Dr. Castel’s gambit is beginning to pay off for both parties.

On Tuesday, his company, Variant Bio, based in Seattle, announced a $50 million collaboration with the drugmaker Novo Nordisk to develop drugs for metabolic disorders, including diabetes and obesity, using data collected from Indigenous populations. Variant Bio will distribute a portion of those funds to the communities it worked with in nine countries or territories, including the Māori, and will seek to make any medicines that result from its work available to those communities at an affordable price.

Experts on Indigenous genetics said the deal was a positive step for a field that has been plagued by accusations of exploitation and a gulf of mistrust.

“In the past, researchers would enter Indigenous communities with empty promises,” said Krystal Tsosie, a geneticist and bioethicist at Arizona State University who runs a nonprofit genetic repository for Indigenous people. “Variant Bio is the only company, to the best of my knowledge, that has explicitly talked about benefit-sharing as part of their mission.”

The concept for Variant Bio was hatched in a Manhattan bar in August 2018 over drinks between Dr. Castel and Kaja Wasik, who had become friends during their graduate studies in genetics at Cold Spring Harbor Laboratory on Long Island.

Though their laboratory research kept them under the glare of fluorescent lights, they shared a zest for international travel, which they indulged during backpacking trips together in Peru and Chile. They dreamed of building a company that could get them to remote places.

At the time, drugmakers were establishing partnerships with biological repositories such as UK Biobank, which contains biological samples and health records from a half-million people living in Britain, in order to hunt for associations between genes and disease.

But these databases are primarily made up of genes from people of European descent.

“What’s the value of sequencing the 500,001st British person?” Dr. Castel said. “There are only so many insights to find by studying the same group of people.”

He and Dr. Wasik were more enthusiastic about recent findings from underrepresented groups, such as the discovery of novel gene variants affecting metabolism that were first identified in Inuit populations in Greenland.

Such variants may be more common, and consequently easier to identify, in historically isolated populations because they confer some functional benefit to people with a certain diet or lifestyle, or simply because of chance events in their history. Yet they can also serve as promising drug targets that will help a wider swath of the global population.

With $16 million in seed funding from Lux Capital, a venture capital firm in New York City, Dr. Castel and Dr. Wasik quit their jobs and began working full-time for their startup. Dr. Wasik hopped across eight countries in Africa, Asia, Europe and the Pacific in the company’s first year, while Dr. Castel, for the most part, dutifully built their software platform from his base in the United States.

They enlisted ethical advisers to develop a benefit-sharing model and went on a listening tour. They knew from the get-go they would have to tread carefully.

In 2007, a member of the Karitiana tribe in Brazil told The New York Times that his community had been “duped, lied to and exploited” by scientists who had collected their blood and DNA, which was later sold for $85 per sample. The tribe members, who said they had been wooed with promises of medicines, received nothing.

Ten years later, there was still no consensus about the optimal way to conduct such work. To protect against so-called biopiracy, many countries ratified the Nagoya Protocol under the United Nations Convention on Biological Diversity, which requires the “equitable sharing of benefits” emerging from genetic resources. But the protocol excluded human genomic information.

During Dr. Castel’s and Dr. Wasik’s trip to New Zealand in 2019, the researchers and community members were troubled by a previous attempt by U.S. researchers to patent a test for obesity risk based on genetic studies carried out in Samoa. The researchers’ universities did not include their Samoan collaborators on their patent application as co-inventors, nor did they have formal benefit-sharing agreements in place with local institutions. (That patent application has since been abandoned, and the researchers said they always intended to share benefits with their partners.)

One of Variant’s first advisers was Keolu Fox, an outspoken geneticist at the University of California, San Diego, who had been harshly critical of the Samoan research.

“This is an extension of all these other forms of colonialism,” said Dr. Fox, who is Native Hawaiian and joined Dr. Wasik and Dr. Castel on their New Zealand outreach trip. He believed that Variant could lead by example.

In the company’s benefit-sharing program, up to 10 percent of a project’s budget goes toward community programs, typically by funding local organizations.

For example, as part of its New Zealand-based study into the genetic causes of kidney disease and other metabolic disorders in the Māori and other people of Pacific ancestry, the company spent $100,000 to fund several local health organizations along with scholarships and scientific conferences for Indigenous people.

“Before Variant came along, we didn’t do that because we couldn’t afford to do so,” said Tony Merriman, a gout expert at the University of Alabama at Birmingham who has collaborated with the company on two projects in the Pacific region.

Dr. Merriman said that he also appreciated that the company ensured that its findings were shared with the community. In French Polynesia, the company’s research has encouraged increased access to a gout medication after concluding that the local population did not have an elevated risk of a fatal drug reaction that had been observed in certain Asian populations.

The new Novo Nordisk deal kicks off a second, longer-term phase of the benefit-sharing program. Communities will share in a 4 percent slice of Variant’s revenue and, if the company is ever sold or goes public, 4 percent of its equity. That percentage is comparable to the royalties that universities receive for licenses to their patents.