But the risks for transgender migrants, in particular, are greater than just the discrimination they face. Nearly 36 percent of transgender people who stayed in a migrant shelter in Mexico reported experiencing some form of violence, according to a 2013 study of 862 migrants conducted by the Mexican National Institute of Public Health. Meanwhile, 57 percent of transgender migrants who did not stay in a shelter reported violence.

The prevalence of violence among this particular group - which accounted for roughly 3 percent of all migrants - surpassed that of women, another vulnerable population. About 27 percent of female migrants who stayed in a shelter reported experiencing violence, but the rate rose to 35 percent for those who did not stop in shelters. The rates were much lower for men -- in that group, 20 percent who stayed in shelters, and 21.3 who did not, reported violence.

The capacity to protect transgender - as well as gay - migrants in shelters appears limited, despite the fledgling efforts to create safe zones.

"The shelters and the state are not prepared to accommodate trans and gay migrants," said Rosember Lopez Samayoa, the director of an HIV-prevention nonprofit organization, Una Mano Amiga en la Lucha Contra SIDA, or A Friendly Hand in the Fight Against AIDS, based in Tapachula, a small city just north of the porous Guatemala border. "If a man arrives dressed like a woman, it can become a huge scandal for them and they really won't know how to register them or treat them."

Lopez's organization is the only known group along the border that works directly with gay and transgender migrants, who often use Tapachula as a launching pad to stop and work until they have enough money to continue on to the U.S., or, more often these days, to a larger city in Mexico.

The persecution that many of these migrants fled from in Honduras and Guatemala trails them to the conservative streets of Tapachula, which Lopez says has seen eight reported murders of gay and trans people from January through May 2013.

Rafael Zavala, the head of the UN Refugee Agency office in Tapachula, said that the organization is planning to document the trend of arriving Central American LGBT migrants, driven by the perception of higher numbers of arriving gay and transgender migrants, and violence against these migrants in Tapachula.

Not all migrants actually come out as gay or transgender, well aware of the danger this revelation could bring, says Lopez. That could explain why in San Luis Potosí, a year-old LGBT-friendly room in a migrant shelter has not been in use for more than two months. More than 60 other shelters plan to replicate the model of this church-run shelter, but according to Geraldine Estrada, an official there, she has not seen gay or trans migrants for months, and the segregated room is now occupied by other people.