The Houston Police Department said the shooting happened under the North Freeway overpass at E. Crosstimbers at about 2:20 a.m.
HPD said one of the victims stumbled into a nearby IHOP to get help, and the second was found at a nearby bus stop.
Witnesses told police someone in a silver car may have been the shooter.
"We got two males shot. We believe (the shootings) are related," HPD Lt. R. Willkens said. "Whether or not there was a silver car that shot him, we don't know that yet."
Willkens said both victims, who are in their 30s and appear to be homeless, are recovering in the hospital.
Police don't have any suspects in custody.