Kendrell Lavar Lyles has been charged with three counts of murder, police said.
Maj. Max Geron announced the charges in a press conference Wednesday. He mentioned Booker by name but did not identify the other two victims.
Booker was shot to death in May, weeks after a video of her being attacked by a mob spread across the internet. Her death drew national attention to the cycle of violence transgender women regularly experience.
Detectives connected Lyles to Booker's death while investigating the two other killings, Geron said.
Both victims were shot to death, one on May 22 and the other on May 23. A tip in the first case led police to Lyles, who was arrested on June 5 in that case.
In the May 23 killing, a witness told police that she drove with Lyles to meet the victim for a drug transaction. As the victim approached the car, the witness said Lyles fatally shot the victim, according to police.
While investigating those cases, detectives concluded that Lyles drove the same kind of car that Booker was seen entering on May 18, the day she was last seen alive.
Cell phone records indicate that Lyles was in the same area as Booker the night she went missing, police said.
Geron said Lyles is also a person of interest in the death of Chynal Lindsey, whose body was found in a lake less than two weeks after Booker's death.
Geron said that police had tied Lyles to Lindsey's case, but he did not elaborate further.
Police initially said Lyles was 34 years old and later corrected his age to 33.
CNN's Jamiel Lynch contributed to this report.
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