He was wanted in connection with a brutal murder that was allegedly part of an MS-13 initiation.
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Gomez is a notorious alleged gang member who was indicted four years ago.
He was arrested without incident. The FBI is crediting public assistance.
Authorities say Gomez and another man murdered a fellow gang member, Julio Matute, inside a home in 2011.
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Gomez and the co-conspirator allegedly struck Matute in the head with a baseball bat, sliced his throat, and stabbed him in the back 17 times with a screwdriver, apparently because Matute was suspected of socializing with a rival gang.
The co-conspirator was subsequently apprehended, charged and found guilty for the Matute homicide.
"The apprehension of Walter Yovany Gomez is a prime example of the close coordination between the public and law enforcement," said FBI spokesman Michael Whitaker. "Gomez will now stand trial for his alleged involvement for a brutal murder, which took a young man from his family."
Gomez is being held in Virginia, awaiting extradition to New Jersey where he was indicted.