Joseph Danclair, 36, was arrested for the death of Antoinette Marin, 43, who was discovered dead inside the Manhattan Broadway Hotel on West 38th Street on Sept. 8, police said.
Police expected Danclair will also be charged later on Friday for the murder of Chrissy Bevelaqua, 35, who was found naked and dead inside the Bushwick Hotel in Brooklyn on July 23, Chief of Manhattan Detectives William Aubry said.
"The hotel rooms were left in similar ways," Aubry said. "We identified him entering those locations and also leaving those locations. When he entered he entered with a female and he exited alone."
Danclair initially told detectives both women overdosed, then he stopped talking and asked to speak with a lawyer, sources said.
Aubry said both women showed signs of trauma around their necks when they were found.
"These women were good women, there's no prostitution involved," Aubry said.
Officers searched for Danclair for a week and, when they caught up with him at one location, he fled, leaving through the backyard and fracturing his foot as he jumped over a fence.
Police eventually tracked down Danclair to his girlfriend's apartment on First Avenue in Kips Bay Thursday night, sources said.
"I didn't have anything to do with it," Danclair mumbled to reporters as he was walked out of the precinct.
Aside from the murders, Aubry said Danclair was a suspect in the rape of two other women — a 41-year-old in Manhattan and a 34-year-old in Brooklyn.
Aubry said he met them in similar ways as Marin and Bevelaqua and that the women "very lucky to be alive."
Both women said their attacker had tattoos similar to Danclair's, according to police. He has not been charged in either rape.
Before Friday, Danclair had been arrested 28 times, officials said. He served about two years in prison on two separate drug convictions in 2003 and 2009, according to the Department of Correction records.
Surveillance video showed him at both hotels where the women were found.
Reporting by Ben Fractenberg, Sybile Penhirin, Nicholas Rizzi and Murray Weiss.