Late in the summer of 2012, while walking his coffee groves on a hillside rising above Santa Ana, El Salvador, Mario Mendoza Corleto noticed something unusual: the leaves on some of his trees were coated with an orange fungus and had begun dropping to the ground. It was “leaf rust,” a form of blight that had pestered coffee farmers in El Salvador since the 1970s. Normally, spraying the trees with fungicide once or twice a year would keep the disease at bay. Not anymore. “This year it was totally different,” Mendoza recounted to me recently. “Spraying didn’t help.”

As the days wore on, the problem only worsened. By September, many of Corleto’s once-bushy trees stood completely bare. Their green fruit hardened in the sun, never ripening into the candy-red cherries that Mendoza’s workers would pick and process into coffee beans destined for specialty roasters. That year, half of the trees on his family’s 100-year-old farm died. The next year, as Mendoza’s remaining trees continued to struggle, he laid off most of his workers. The harvest was a quarter of its usual size.

What happened to Mario Mendoza Corleto played out all across El Salvador, as well as Honduras and Guatemala: ground zero for the Western hemisphere’s most prized coffees.

For the next two years, la roya, as leaf rust is known locally, tore through Latin America’s coffee farms, infecting as much as half of the total acreage, inflicting over $1 billion worth of damage, and helping to trigger a migrant crisis as farmers and farmworkers fled economic ruin.

Coffea arabica is one of the least genetically diverse — and therefore, least resilient — modern crop species on earth.

How did leaf rust suddenly gain the upper hand? Researchers think the disease, a fungus that evolved with coffee trees in the forests of Ethiopia, may have undergone a major recent mutation to become more aggressive. Meanwhile, climate change created the warm, wet weather conditions that sent it into hyperdrive, breaking through coffee’s natural disease resistance.

Leaf rust’s sudden fury did more than devastate individual farmers. It exposed a surprising weakness at the root of the $175 billion global coffee business. Coffea arabica is one of the least genetically diverse — and therefore, least resilient — modern crop species on earth. The trees that growers plant today, especially for the most coveted coffees, haven’t changed much since the 19th century. As one insider put it, “the whole industry is running on software that’s 150 years old.”

Since 2012, the leaf rust has retreated, thanks to a combination of milder weather and diligent control efforts in the fields. But researchers are certain that it will return — some believe as soon as next year — which would mean walloping farmers already suffering from both low prices and yields that haven’t fully recovered from the last outbreak.