Firefighters responded to the 200 block of Marina Drive after the fire erupted around 5 p.m. Authorities said the boat was at a fueling dock.
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"A 35' pleasure craft was well involved with fire upon the arrival of fire department units. The fire occurred in close proximity to the fuel dock near Fire Station 21," according to the Long Beach Fire Department.
People on nearby boats said they heard a powerful blast.
Clouds of thick black smoke and flames poured from the boat as firefighters arrived to battle the blaze.
Authorities confirmed two women in their 60s died, and three others - two men and a woman - were hospitalized with burn injuries.
Long Beach firefighters extinguished the blaze with help from the Orange County Fire Authority.
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The boat was destroyed by the fire. Investigators are examining the charred vessel to determine what went wrong.
"Initial reports indicated they were in the process of doing some type of refueling operation, or had just completed a fueling operation," LBFD Capt. Jake Heflin said. "That's obviously all part of the ongoing investigation."