Roberto Ramirez, 21, is charged with aggravated sexual assault.
Police identified him as the suspect in the rape after a DNA match came through in CODIS.
According to police, Ramirez approached the 31-year-old victim as she was walking to a bus stop at Wayside and Lawndale around 1 p.m. on February 22, 2012.
The victim said he asked her to go with him to his house, but she ignored him.
When she boarded the bus, the victim said the suspect followed her.
The victim got off the bus in the 5600 block of Old Spanish Trail, to take another bus to her mother's house.
She said the suspect followed her there, too, and as she was waiting at the stop, he hit her over the head with a plastic bag containing a glass bottle.
The blow caused a laceration over her right eye, and the victim said she was in severe pain.
She said Ramirez then grabbed her and pulled her to a weeded area behind the bus stop, where he sexually assaulted her.
After the assault, the victim said the suspect took her clothes and walked off.
She ran to a nearby business, wearing only a bra, and called for help.
The victim was taken to the hospital, where a rape kit was performed.
On March 9, CODIS found a match between a DNA sample from the rape kit and a sample taken from Ramirez after another crime, police said.
Ramirez has prior convictions of theft, robbery and drug possession.
Investigators said they were led to him in Abilene by a Crime Stoppers tip. They found him at a home with his girlfriend and other family members.
It was not clear when Ramirez would be transferred back to Houston. His bond was set at $50,000.
There have been three other sexual assaults at or near Metro bus stops this year, but so far, police have not named any suspects in those crimes.
By: Sherry Williams KHOU 11 News