A tenant in the house woke up and smelled smoke, but found the door to the women's apartment locked.
Officers forced the door open and found 77-year-old Dorothy Reinhard and her 60-year-old daughter, Elaine Moore, unconscious on the floor.
The victims were transported to Stony Brook University Medical Center.
The county medical examiner will determine the exact cause of death.
Suffolk County police are investigating the blaze, but authorities say it does not appear to be suspicious.
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