ORLANDO — A former astronaut who commanded space shuttle Discovery’s second-to-last mission died after a water scooter crash involving his sons near Pensacola Beach.

Alan Poindexter, 50, died Sunday after a scooter driven by his 26-year-old son, Zachary, struck the back of a water scooter the former astronaut was riding.

‘‘They were both moving and for some reason Captain Poindexter stopped his watercraft and Zachary for some reason didn’t see him stop,’’ said Stan Kirkland, a spokesman for the Florida Fish and Wildlife Conservation Commission.

‘‘Zachary’s watercraft went up and struck Captain Poindexter.’’

Another son, Samuel, 22, was on Captain Poindexter’s scooter. Captain Poindexter and Samuel were thrown into the water. A boat picked up Captain Poindexter and took him to shore. He was talking and complaining about rib injuries but he lost consciousness and was pronounced dead at a nearby hospital.

Captain Poindexter was selected to be in the astronaut corps in 1998.

The accident happened in a bay between Gulf Breeze and Pensacola Beach in Florida’s Panhandle, where Captain Poindexter had been vacationing.

Captain Poindexter’s family has close ties to the area. His wife, Lisa, is from Gulf Breeze, and Captain Poindexter reported to flight training in Pensacola after college.

No charges were filed, Kirkland said, and an exact cause of death would be determined by the medical examiner.

After retiring from NASA in December 2010, six months before the shuttle program ended, Captain Poindexter took a job as dean of students at the Naval Postgraduate School, where he had graduated in 1995.

Captain Poindexter was selected to be in the astronaut corps in 1998.

He flew on his first mission a decade later when he was a pilot aboard Atlantis’s mission to install the Columbus laboratory at the international space station.

He commanded Discovery’s second-to-last flight in April 2010, a mission to resupply the space station.

The shuttle program ended in July 2011.

The astronaut’s father is retired Navy Admiral John Poindexter, national security adviser under President Reagan. Captain Poindexter was born in Pasadena, Calif., and grew up in Coronado, Calif.

Captain Poindexter, who attended the Georgia Institute of Technology, became a naval aviator in 1988.

He made two deployments to the Arabian Gulf during Operations Desert Storm and Southern Watch.

He worked as a test pilot before he was selected to become an astronaut in 1998.