Officials identified 32-year-old Anthony Lamar Jones early on as a suspect. Investigators say they had him under round-the-clock surveillance.
Police say Jones was booked on murder, kidnapping to commit rape, rape, and lewd or lascivious acts on a child. Officials believe he acted alone; no other suspects have been named.
Jones was arrested a couple of blocks where a surveillance camera took the last known photo of Genelle Renee Conway-Allen before she disappeared.
Jones was rousted out of his bed early Friday morning at his mother's apartment in a residential complex near the 1100 block of East Tabor Avenue.
Neighbor Jennae Rincon told us that an officer knocked on her door at around 6:30 a.m., "He asked me questions, showed me pictures of a man who they thought was the perpetrator and showed me pictures of the girl and asked if I had ever been to Crown Barber," Rincon said.
Crown Barber turned out to be a men's hairstyling shop. Owner Randy says Jones rented a station from him. Police also appeared there early in the morning during the operation. They took evidence from the shop and boarded up the windows and door.
John Hardeen is a contractor who helped with the electrical wiring in the salon. He was shocked to learn about the arrest, "They just seemed like nice guys," Hardeen said. "Just, nothing seemed out of the ordinary."
Police also roped off a house on Clipper Lane in the early morning hours, and investigators brought out more evidence from the home.
Fairfield police said they had identified Jones as a suspect early in the investigation.
"Since that time, he's been under 24 hour surveillance," Sgt. Rebecca Belk said. "Therefore, there was no danger to the public during the investigation
Jones' mother's apartment, the place of his arrest, is a few blocks away from a market. Earlier this week, police released a picture of the 13-year-old, which was taken by a police surveillance camera across the street from the market.
The seventh-grader was reported missing around 5:45 p.m. on Jan. 31 by her guardian at the foster home in nearby Suisun City where she lived. A passerby found her naked body in Alan Witt Park the next morning.
It wasn't until earlier this week that police identified her as the missing 13-year-old.
Hours after the arrest of Genelle's accused killer, more than 300 people gathered just a few yards from where her strangled body was discovered in the park.
"I miss her really, really bad," Cassandra Luna said. "She was my best friend."
The teen's father, Josh Allen, says he and Genelle's mother had trouble with drugs and lost custody of her last year. But in spite of their obstacles, he says she kept a smile on her face.
"Just a great kid," Josh said. "Very loving and very affectionate, and I love her with all my heart."
ABC7 News spoke with Jones' mother, she said she is devastated after learning of his arrest. She said he was raised in a family that went to church every Sunday and that she just can't imagine he would do anything like this.
Jones' arraignment court date is scheduled for February 13 at 1:30 p.m. and he is being held with no bail.
(The Associated Press contributed to this story)