Violent clashes at the US-Mexican border, with refugees throwing rocks and police firing tear gas, are the latest sign of intensifying trouble in Central America. Why are its people fleeing? Some of the reasons are easy to identify. Decades of exploitation by US-owned corporations left a legacy of political oppression and weak coffee-and-banana economies. Militarization in the 1980s suffocated democratic movements. Gang violence has spread. Climate change is eating away at natural resources.

One of the most important factors fueling this crisis, however, is also among the most overlooked: gender-based violence. In recent years, this plague has reached dramatic proportions. “It is taking on a magnitude and a level of cruelty that is devastating Central America,’’ a United Nations official asserted in 2016. He spoke as the UN released a report showing that among all countries in the world that are not at war, the three with the highest rates of violence against women are Honduras, Guatemala, and El Salvador.

Many of the Central American refugees now making their way toward the United States are female. They have special reasons to flee. In Honduras, which is the size of Ohio, a woman is murdered every 16 hours. El Salvador has reached an even grimmer position on the horror list: world’s highest rate of “femicide.’’ A survey concludes that one in every four women in rural Nicaragua, and one in five who live in cities, has been physically attacked. The attorney general of Guatemala, where the murder of women is a daily occurrence, estimates that half of the female victims have been lured or forced into the sex trade, and then killed for some reason — or for no reason at all.

Many female victims in Central America are assaulted or killed by gangs that roam where law has lost its grip. Societies that have long been harshly patriarchal revert to their worst instincts when people can be killed with impunity. That is the effective reality in large parts of Honduras, El Salvador, and Guatemala.

Women in Central America who escape the clutches of criminal gangs often face violence at home. Rates of adolescent pregnancies are among the highest in the world. Public health workers say this reflects a culture in which some fathers, stepfathers, and neighbors feel free to molest girls. A UN representative in El Salvador recently called the sexual abuse of children there a “very profound, difficult, and serious’’ problem. That applies to much of Central America. “It’s huge,’’ a judge from the Nicaraguan town of Leon told a recent interviewer. “Every day we process sex crimes.’’

Two prominent Central Americans represent the forces arrayed against women there. The most obvious is President Daniel Ortega of Nicaragua, whose stepdaughter has accused him of sexually abusing her for more than a decade beginning when she was eleven. Ortega’s permanence in power is a potent symbol of the immunity that protects sexual predators in Central America.

At the other end of the spectrum — on the receiving end of violence — was Berta Caceres, the environmental activist who was murdered in 2016 as she waged a campaign against the construction of a dam in Honduras. Her case attracted worldwide attention and resulted in rare arrests and convictions, but those who ordered her killing remain at large. They join a growing number of men in Central America who take advantage of the fact that they can kill women with little fear of punishment. That has a political impact, since in much of Central America, women are emerging as leaders of social movements. Many are young, among them Valeska Valle, a 22-year-old accounting student who is helping to direct anti-government protesters in Nicaragua, and Lenina Garcia, who last year became the first female president of the student body at Guatemala’s most important university and is using her position to organize marches against corruption and impunity. They have given a distinctly feminine face to political protest, turning political repression into another form of gender-based violence.

These threats to Central American women — assault at home, abuse at the hands of criminal gangs, and violent punishment for those who protest — propel many to flee. “Sexual violence is the major push factor,’’ concluded a study conducted at the National Autonomous University of Mexico. When researchers asked female refugees why they fled, most cited rape, gender-based violence, and fear of sex trafficking.

As these women take to the unarmed road of flight, they risk other forms of abuse. They are easy prey for predators on both sides of the law. Experience has prepared them for it. A plague of violence against women is spreading through Central America. As long as it rages, mothers and daughters will keep fleeing.

Stephen Kinzer is a senior fellow at the Watson Institute for International and Public Affairs at Brown University.