The incident happened just after 4 a.m., according to the Los Angeles County Sheriff's Department.
The victim was transported to a hospital after being struck twice when the suspect shot at the train, a sheriff's spokesperson said.
The train operator was initially transported to a hospital in critical condition. Authorities said the train operator is in stable condition.
"We're not completely sure if the driver was targeted or if it was a random type of shooting, we don't know that right now, that's why they're downloading the video to get a better picture of what exactly happened," said Ramon Montenegro, a spokesperson for the LASD Transit Services Bureau.
Authorities released a photo of the suspect Friday afternoon and announced a $25,000 reward was being offered for information that leads to the capture of the suspect.
L.A. County Supervisor Hilda L. Solis announced she was offering a $10,000 reward for information that leads to the capture of the suspect.
Phoenix police officer fatally shoots armed man holding baby son as hostage
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Metro's Indiana Station was closed earlier as deputies established a perimeter and searched for the shooter.
Train service was suspended between the Soto and Maravilla stations, Metro said on Twitter. Riders were urged to use Line 30 for alternate service.