Kendrell Lavar Lyles, 34, 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.
Booker was last seen on May 18, when she got into a car matching the description of Lyles' car, police said.
Cell phone records indicate that Lyles was in the same area as Booker the night she went missing, police said.