John Bittrolff, 48, of Manorville, N.Y., was arrested Monday. He has been charged with killing Rita Tangredi, 31, and Colleen McNamee, 20, of Holbrook.
Both women had been arrested for prostitution not long before they were killed. Tangredi had no known address at the time, police said.
Tangredi's body was found in late 1993. McNamee's was discovered in January 1994, a few weeks after her parents reported her missing.
Suffolk County Police said in a statement that investigators have nothing at the moment to link Bittrolff to Long Island's largest unsolved homicide investigation. In 2010 and 2011, human remains were found in Gilgo Beach State Park on the South Shore, in neighboring Oak Beach and in Jones Beach State Park to the west in Nassau County.
Some of the bodies are still unidentified, while others are known to be women who worked as prostitutes. Investigators believe they were dumped by a serial killer active over 20 years.