Police are also looking for the officer's mother who lives with him in the home.
A husband, wife and two sons lived in the home on 238th Street, and now, it has turned into a crime scene with investigators trying to unravel a mystery.
Heavily armed tactical officers with guns drawn, and expecting a possibly dangerous standoff, moved in quickly and took a 25-year-old man who lived in the home into custody.
"Other officers entered the house under the premise that other people were inside who needed help. At that time the two bodies were discovered," said Detective Lt. Kevin Smith of the Nassau County Police Department.
One man's body was found in the kitchen, the other man's was found in the basement.
A relative says he called police after he went into the house to check on his nephew, a New York City Corrections Officer, who had failed to show at his job on Rykers Island.
"I knocked on the door, I assumed someone just called the police," the relative said.
During the day, fellow corrections officers huddled together waiting for details.
Investigators brought in a special cadaver dog from Suffolk County, and officers worked inside the house and in the surrounding neighborhood hoping to solve an added mystery.
Police revealed that the wife and mother who also lives at the home is missing.
She is Rose Ormejuste. She also goes by Maryse.
Investigators say she is about 60-years-old and may be driving a missing car, a 1998 Gray Lexis ES 300 with New York license CEF8130.
Her friend and neighbor Azale Mathie is disturbed by the tragic events.
"It's sad, I don't know what happened. I talked to the lady Saturday, Saturday morning. She didn't tell me anything," Mathie said.
"The last time anyone had heard from the mother was sometime Monday morning. She had a phone conversation with other family members, after that, I am unsure," Det. Lt. Smith said.