Alvin Latham survived the storm but is accused of fatally stabbing and beating the captain, Raymond Leiker, last week in the Gulf of Mexico, about 30 miles southeast of New Orleans.
Latham was scheduled for arraignment Monday in state court on a second-degree murder charge.
"I think things just went way out of hand. With the weather so bad and the boat sinking, they were just fighting for their lives," said Capt. Curtis Bowers of the Plaquemine Parish Sheriff's Office.
Bowers said the men were heading into the safety of a bay to escape the squall when the motor was swamped and the boat started taking on water.
Inside the cabin, the men began fighting over the only life jacket.
Latham has confessed to grabbing a knife and pipe and striking at the captain, who fell back into the sea, Bowers said.
The body of Leiker, 34, was found Friday floating about 30 miles from the site of the sinking. The discovery led police to arrest Latham.
Latham, 46, originally told police the captain had gotten entangled in nets as the boat went down.
The Coast Guard has scanned the area for the missing boat, but there is little hope it will be recovered, Bowers said.