In a statement, Hong Kong police said that both captains, aged 54 and 56, had been charged separately with 39 counts of manslaughter.
The pleasure boat Lamma IV, and a high-speed ferry, the Sea Smooth, collided in October 2012.
The crash killed 39 people, including several children.
92 passengers were injured.
"Police arrested the two coxswains and other five male crew members aged between 50 and 63 on October 2 last year," the statement said. "The coxswains were charged today (April 11) after Police sought legal advice and they will appear before Eastern Magistrates' Courts this afternoon. The five crew members will answer bail in mid-April."
The collision was the worst maritime accident in Hong Kong since 1971, when an accident on a ferry left 88 people dead.
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