The Colorado Springs Police Department said that Lee and Stella Vigil, both in their 70's, were reported missing around 8:30 p.m.
Family members and officers responded to the area and discovered the couple's vehicle at the trailhead.
The couple's bodies were found by police officers and the El Paso County Search and Rescue at 12:25 a.m. adjacent to Fountain Creek just off the Santa Fe Trail.
Police said both were discovered dead from "apparent gunshot wounds."
Detectives from the department's Violent Crimes Homicide/Assault Unit responded to assume control of the investigation, according to FOX21.
No additional details were released by police.
Those who hike frequently on the trail said Saturday they were shocked by the news.
"Up until today I usually feel pretty good. You have to be a little careful, sometimes there are some sketchy people," Michael Hollenbeck who recognized the couple told KRDO-TV. "It's sad, it's upsetting, I think I've seen them on the trail before."