The trees of the International Cacao Collection grow here in an astonishing diversity of forms, bearing skinny cacao pods with scorpion-stinger protrusions, spherical green pods that could be mistaken for tomatillos, oblong pods with bumpy skin resembling that of the horned lizard — all in colors ranging from deep purple to bright yellow.

Within each of these pods are seeds that yield something beloved by billions: chocolate.

But despite this diversity, few cacao varieties are widely cultivated, and that’s a problem: Like many other crops, cacao is under constant threat from diseases and environmental challenges exacerbated by our tendency to grow only a few varieties with similar or identical genetic traits and defects.

“Most varieties produced worldwide belong to a narrow set of clones selected in the forties,” said Wilbert Phillips-Mora, who oversees this collection of 1,235 types of cacao trees and heads the Cacao Genetic Improvement Program at C.A.T.I.E. (an acronym in Spanish for the Tropical Agricultural Research and Higher Education Center).

A narrow gene pool means that most commonly cultivated varieties of cacao are susceptible to the same diseases, and these blights can spread quickly.

Cacao production brought relative prosperity to the Caribbean coast of Costa Rica until the late 1970s, when farmers began to notice that pods on their trees were developing a fuzzy white fungal coating and eventually mummifying.

The fungus — Moniliophthora roreri, also called monilia or frosty pod rot — soon spread around the country, and by 1983 Costa Rican exports of dry cacao beans had declined by 96 percent. The industry here has never recovered.

The calypso singer Walter Ferguson even wrote about it. “Monilia, you’ve come to stay,” he sang, “and all you bring is hungry belly/You say you no going away, ‘til you bring me down to poverty.”

Folk songs about fungi may be rare, but the devastation to the region’s primary industry was profound. And though the Costa Rican outbreak is history, the fungus continues to spread.

“For me, the cacao industry is in permanent risk, because intentionally or unintentionally this disease could be spread in just one flight,” said Dr. Phillips-Mora. Increasing travel and commerce in the developing world have provided new pathways for infection.

He believes the most recent confirmed outbreak — in Jamaica in September 2016 — may have been the result of marijuana traffickers moving covertly between Costa Rica and Jamaica, unwittingly grabbing infected cacao pods as snacks for the boat ride home.

That outbreak was the first confirmed outside of Latin America, and it has demonstrated the fungus’ ability to survive more distant travel than previously known. Other cacao-producing regions, such as West Africa — the source of virtually all the cacao that ends up in mass-produced products like Hershey’s Kisses and M&M’s — may face similar outbreaks.

Even without frosty pod rot, cacao is a problematic crop. Other diseases — witches’ broom, black pod, cacao swollen-shoot virus — also afflict the tree. Climate change promises to further exacerbate problems with tropical plant pathogens.

These difficulties make cacao ever less appealing to producers; yields and profits are low, and the average cacao farmer is aging. The next generation seems to be abandoning the family business.

Yet demand for chocolate is rising, especially as gargantuan markets like China and India indulge a taste for what used to be a treat primarily for American and European consumers. A chocolate shortage may be on the horizon.

That is where Dr. Phillips-Mora’s project comes in. The genetic diversity of cacao, on full display in the International Cacao Collection at C.A.T.I.E., may avert a chocolate crisis.

A Hybrid Solution

In the early 1980s, Dr. Phillips-Mora worked to identify the most naturally tolerant and productive cacao trees, then painstakingly hybridized the candidates to create novel varieties.

Breeding hybrid cacao clones is a lengthy process, and experts worldwide have largely failed in this endeavor. But in 2006, Dr. Phillips-Mora released his first batch of hybrid cacao varieties.

In terms of disease resistance and yield, the differences were astonishing. Dr. Phillips-Mora’s six hybrids produce on average about three times more cacao than standard varieties; under ideal conditions, the most prolific hybrids can produce six times more cacao.

After an 11-year trial, a hybrid called C.A.T.I.E.-R6 experienced a 5 percent frosty pod rot infection rate, compared to 75 percent infection for a control variety.

“Our goal is not just to produce cacao,” Dr. Phillips-Mora said. “It’s also to give the basic living conditions to the farmers. Most cacao farmers are very poor, because the system is based on material that doesn’t have good yielding capacity.”

Trees that buck this trend could make the family business look more enticing to the next generation of cacao growers. The C.A.T.I.E. hybrids are now growing in all Central American countries, as well as in Mexico and Brazil.

Agricultural yield and disease resistance may benefit farmers, but a cacao crop is worthless if it produces bland or foul-tasting chocolate. Chocolate is the epitome of gastronomic hedonism.

But unlike nearly every other modern effort to increase crop yields, Dr. Phillips-Mora’s breeding program incorporates fine flavor as a prerequisite. Cacao varieties that don’t impress expert palettes are discarded, no matter how well they grow.

The result of this protocol is that unlike many other crops favored for agronomics — the Red Delicious apple, the Cavendish banana — C.A.T.I.E.’s cacao actually tastes good.

Chocolate makers are beginning to roast and package Dr. Phillips-Mora’s varieties. Dandelion Chocolate, based in San Francisco, recently released a bar made from a mix of all six C.A.T.I.E. hybrids.

“I think honestly it’s going to be one of our most popular bars,” said Greg D’Alesandre, who heads cacao sourcing at Dandelion. “It has this nice balance of chocolaty and caramel notes, but it keeps it very accessible.”

Dr. Phillips-Mora’s hybrid cacao varieties do not offer a perfect solution to all the crop’s challenges.

They cannot all self-pollinate, and some of the beans are small; they haven’t been properly tested in Africa or Asia, and they are not yet resistant to all the pathogens that afflict cacao globally. Field trials are nearing completion on a new batch of clones bred to address some of these issues.

Moreover, the current roster of C.A.T.I.E. clones were bred in response to known cacao production threats; the future will present new demands. Pathogens evolve. Unstable political situations in the developing world can affect agriculture. Climate change will alter landscapes in unpredictable ways.

The solution is not to replace all cacao with the six available C.A.T.I.E. varieties, but to be able to continue to diversify the cacao materials growing worldwide. Like the Svalbard Global Seed Vault, the International Cacao Collection is a contingency against future disasters of unknown character.

Whatever fungal mutation may arise, wherever drought may strike, however chocolate tastes may change — there will likely be cacao genes somewhere in the collection that can form the basis of new hybrids to meet future challenges.

Still, Dr. Phillips-Mora worries about the future.

Though he works with deep-pocketed companies like Mars, Nestlé and Hershey, the funds he receives are generally earmarked for specific research projects rather than for the maintenance of the collection and program for the future.

He estimates that he receives less than 5 percent of the funds necessary for proper upkeep of the collection each year. So although Dr. Phillips-Mora retired three years ago, he plans to keep working until the solvency of the collection is ensured.

“I will be very happy when I leave this institution to know that the collection will be protected financially,” he said. “It’s a treasure for everybody, for all the cocoa lovers.”