In 2004, Flanagan successfully defended a nurse, Amy Brunner, accused and ultimately acquitted of involuntary manslaughter.
Brunner was accused of leaving a syringe full of propofol out for another nurse to administer to an 80-year-old cancer patient who died within minutes of receiving the shot.
"I'm probably the only attorney in town that has successfully tried a propofol case involving death," Flanagan told TMZ earlier this month.
The charges end an eight-month investigation that included countless interviews with Jackson's previous physicians, coordinated raids on Murray's home and offices in Texas and Las Vegas, and a weeks-long wait for the results of a toxicology report.
Defense attorneys not affiliated with the case said the prosecution ultimately will have a difficult case to make once they go to trial.
"The prosecution has to prove gross negligence and that Dr. Murray acted recklessly," said Laurie Levinson, a professor at Loyola Law School.
"They have to show more than just malpractice," she said. "They have to prove criminal negligence. That's not going to be easy. Terrible accidents happen all the time. Was [Murray] warned that something could happen? Did he know the risks?"
Involuntary manslaughter, she said, was "the lowest level of homicide in California," carrying a potential sentence of 2 to 4 years in prison.
According to police reports, Murray found Jackson dead in the singer's Los Angeles rental home before administering cardiopulmonary resuscitation and requesting that a Jackson employee call 911.
In October, the coroner's office released a statement saying Jackson died from an overdose of the hospital-grade anesthetic propofol.
The coroner also cited the powerful sedative benzodiazepine as contributing to the singer's death. A toxicology screen and search of Jackson's home found several other drugs in the singer's body and bedroom.
Murray was hired to accompany Jackson for a scheduled series of concerts to be held in London last summer. Jackson died just weeks before the tour was to begin.
Murray has denied any criminal wrongdoing.
"We continue to maintain that Dr. Murray neither prescribed nor administered anything that should have killed Michael Jackson," said Miranda Sevcik, a spokeswoman for Murray's legal team.
ABC News' Jim Vojtech and Kaitlyn Folmer contributed to this report from Los Angeles.