Jerry Nehl Boylan caused the deaths of those aboard the Conception "by his misconduct, negligence and inattention to his duties", says the indictment.
Prosecutors allege the 67-year-old failed to have a night watchman or conduct fire drills as required by law.
All 33 passengers and a crew member sleeping below deck died.
Mr Boylan was among five crew who managed to escape the blaze on the 75-ft (23m) vessel off Santa Barbara on 2 September 2019.
He is expected to surrender to the authorities at a later date. Each charge of seaman's manslaughter carries up to 10 years in federal prison.
A US National Transportation Safety Board (NTSB) investigation determined the fire began in a middle deck area where lithium-ion batteries were being charged, though it was unclear exactly what ignited the blaze.
