The gunman, flanked by two companions in hooded sweatshirts, walked into the New Gethsemane Church of God in Christ in Richmond Sunday, scanned the pews and fired about five shots, hitting the two teenagers in front of about 100 people, Richmond police Sgt. Bisa French said.
No arrests had been made or suspects named, police said.
The city has already seen seven homicides in 2010, and garnered national attention because of the alleged gang rape by as many as 10 people of a 16-year-old girl outside an October homecoming dance at Richmond High School, with as many as 20 bystanders allegedly watching.
Charles Miller, a 64-year-old deacon at the church, said members of the congregation were about to tell the men to take off their hoods when the shooting began.
"I was listening to the choir and all of a sudden there was a 'pop pop pop pop pop,'" Miller told the San Francisco Chronicle. "Everyone hit the floor. I didn't know the shooting was inside the church at first, until I heard all of the hollering and screaming."
The 14-year-old was hit in the shoulder and the 19-year-old was struck in the leg, French said. Both victims, whose names haven't been released, were hospitalized and were expected to survive. There were no other injuries.
Investigators believe the men were targeting someone in the church but don't know if the two who were hit were the intended targets, French said.
French said investigators were interviewing witnesses to see if anyone recognized the men.
A handful of congregants returned to the church after police processed the crime scene and finished the service.
"We went on and had church anyway," Miller told the Chronicle. "We were giving thanks that nobody was killed. We wanted to go and serve the Lord anyway."
The small, off-white two-story church is surrounded by a red-and white wrought-iron fence in a residential section of Richmond, a city of 103,000 on the eastern Bay shoreline north of Oakland and Berkeley.