Migrants who now chance the crossing typically get out of vehicles before checkpoints and try to walk around them on dirt trails.
"Some chapines just went by!" one Mexican woman, using a common nickname for Guatemalans, recently told a group of journalists trudging along a back path.
The troops now also mount foot patrols along mountain trails, hiking deep into cool, high-altitude pine forests outside of Comitan. The soldiers find empty water bottles, discarded food packaging, abandoned campsites and other indications that people have been there. The migrants have usually moved on.
"Unfortunately, the coyotes know our every move," said Lt. Alejandro Romero, a 20-year Mexican army veteran who was heading a national guard detachment at the checkpoint outside Comitan.
Many residents are themselves from families in the smuggling business, and they use walkie-talkies to send warnings when troops are near. Still, only a limited number of migrants can hike around the checkpoints.
"The main roads are secure," Romero said, "and that means it is very hard for large groups to get through."
How long that will continue remains unclear.
Mexican President Andres Manuel Lopez Obrador -- who took office last December vowing to provide refuge and jobs for Central Americans -- has been facing growing criticism at home that the crackdown amounts to doing the Trump administration's dirty work. Catholic bishops in particular have accused Lopez Obrador of constructing a virtual wall along the border with Guatemala.
In Gracias a Dios one recent afternoon, there was hardly a soul on the street. Hotels and shops were mostly deserted.
"It used to be very lively here," said Hernandez, the mayor. Wearing a tank top and shorts and seated in a storage room inside his desultory restaurant, he flashed a wry smile that showed gold dental bridgework. "Now the streets are empty. Very few people are trying to cross. I would say my business is down 70%. I think the coyotes are all taking a break."