An arrest warrant is imminent for Jose Carrasquillo, 26, charging him with rape and related offenses in connection with the attack on the 11-year-old.
He's now being held on unrelated charges.
Police announced Tuesday that DNA samples link Carrasquillo to the scene of the rape. They found an blood stain and a fingerprint on a discarded toilet in the yard where the girl was raped.
"Which indicated to us that Mr. Carrasquillo had, in fact, been there," said Capt. John Darby of Special Victims.
Evidence linked to Carrasquillo was also found in the young victim's underwear.
Police say there were also key pieces of evidence left behind, including his sunglasses. They were able to extract DNA samples from the sweat on those sunglasses.
Furthermore, investigators say the shorts Carrasquillo was wearing the day he was arrested had blood stains on them that matched that of the young victim.
Authorities plan to announce the charges against Carrasquillo at a Tuesday afternoon news conference.
Police say Carrasquillo can be seen on surveillance video walking alongside the 11-year-old victim as she walked her little sister to daycare back Monday, June 1st.
Minutes later, investigators allege Carrasquillo dragged her down an alleyway and brutally raped the child in a secluded backyard.
RELATED VIDEO: Rape suspect seen on surveillance video
An all-out search was launched for the suspect. Days later, Carrasquillo was spotted by David Vargas, 18, and Fernando Genuall, 19, in the area of Front and Clearfield. They recognized him and attacked him, holding him until police arrived.
RELATED VIDEO: Carrasquillo's beating caught on video
Vargas and Genuall each received rewards of nearly $6,000 for their part in Carrasquillo's capture.
Carrasquillo will also be charged with groping a 15-year-old girl outside the Kensington Creative and Performing Arts High School on June 1st, just an hour before the rape of the 11-year-old.
Police say the girl has now identified Carrasquillo as the man who groped her.
After the girl was groped, police say the man went into the school, sat down in the cafeteria, and had breakfast.
In a statement released by the Philadelphia School District, officials say the girl saw the intruder and started to scream. That caused the man to run out of the school.
Police say they have two more cases that may be linked to Carrasquillo. They add, they're going back through years of evidence to see if Carrasquillo is linked to those.
They're now wondering if they have a serial rapist on their hands.