The bicyclist was hit by an outbound 27-Bryant bus that was turning onto Bryant Street near 11th Street around 8:40 a.m., Muni spokesman Paul Rose said.
The cyclist was pronounced dead at the scene.
There were about three dozen passengers on board the bus. No injuries to passengers were reported, Rose said.
The passengers were transported to another bus, while the driver was held for questioning, he said.
The operator will be placed on non-driving status and undergo testing for drugs and alcohol, as is normal procedure in accidents, Rose said.
Muni transportation director Ed Reiskin issued a statement this morning expressing his condolences for the death.
"Speaking for the San Francisco Municipal Transportation Agency and its 5,000 employees, I express our deepest sympathy to the family and friends of the person killed near Bryant and Division streets in the tragic accident this morning involving a Muni bus," Reiskin said.
The intersection remained closed as of 11:30 a.m.
The 27-Bryant, 47-Van Ness and 9-San Bruno bus lines were being re-routed around the fatal accident, Rose said.
