28-year-old Yusef Ibrahim was arrested late Sunday afternoon in Bayonne, New Jersey.
He has been charged with two counts of desecration of human remains and two counts of murder.
The bodies were discovered around 5:00 p.m. Friday at a vacant home on the 1100 block of Harding Highway in Buena Vista Townhip.
Police say both bodies seem to have suffered a single gunshot wound.
As the investigation progressed, Ibrahim was identified as the prime suspect.
Police learned that he was driving a white Mercedes Benz that belonged to one of the victims.
Authorities say the Mercedes Benz was located by the Philadelphia Police Department at 4110 Penns Grove Street in Philadelphia.
The vehicle was abandoned and set on fire.
Assistant Prosecutor John Maher approved desecration of human remains charges against Ibrahim.
Authorities won't release the victims' identities until family members have been notified. They do identify them as 25 and 27-year-old Jersey City residents.
Friends say the victims are originally from Egypt and moved to New Jersey recently. They were last seen Monday night at a house gathering.
Friends say they knew something was wrong when the men didn't show up for work Tuesday morning.
A motive has not yet been released and the investigation is ongoing.