Alain Salas, 40, was arrested Monday afternoon by school police at the request of the FBI. He is being held without bail and is expected in court on Wednesday.
"We are familiar with the fact that the FBI had been investigating a case and had arrested the individual," said Superintendent John Deasy.
The FBI began investigating Salas in December when it received allegations of online communication with a 15-year-old at the school. Investigators said the dean of students was notified.
The FBI said Salas has not been formally charged, but is being held on suspicion of having contact with a minor with the intent to commit a sexual offense.
According to Salas' Myspace page, he is a graduate of Fremont High and has been a softball coach for 20 years. He is also a special education assistant.
One of his softball players said Salas is a great coach, and she believes he is being falsely accused. Other students also find it hard to believe he would do anything wrong.
"He was always very respectful," said student Tania Gonzalez. "He never crossed the line, especially with young ladies. He knew his boundaries as a coach as well. I know a personal friend where he was always there for her when she was going through tough situations family-wise."
Other students said they find the allegations disturbing.
"They told me yesterday and I was in complete shock, I can't believe that's happening at our school," said one student.
"There's teachers like that, that shouldn't even be allowed to be teachers at school and have contact with minors," said another student.
Salas is the fifth arrest within the district, which was touched off by the sex abuse scandal at Miramonte Elementary School in South L.A. Two teachers at that school have been accused of lewd acts on students.
Former third grade teacher Mark Berndt and former second grade teacher Martin Springer were both arrested about two weeks ago. Springer has been released on bail.
Paul Adame, a Janitor at Germain Street Elementary School in Chatsworth, was arrested, accused of committing a lewd act on a child.
Third grade teacher Paul William Chapel from Tellfair Elementary in Pacoima was also arrested last October.
Deasy said he doesn't believe there is anything systemic within the district, but that there is currently more awareness and more people are coming forward to report sex abuse allegations.
"I think we had a whole era where we hoped things would go away," said Deasy. "That's not this administration's era. This administration, when we know of something, we act on it."
The superintendent also said the district is looking at ways to improve its screening measures when it comes to hiring new employees.
"I don't think the people of Los Angeles need to be concerned about the safety of their schools," said Ernie Allen, president of the National Center for Missing and Exploited Children.
Allen says high-profile cases raise awareness. Children come forward when they know they are not alone.
"The latest estimates are that two out of every three cases of child sexual abuse and exploitation are never reported to the authorities, and these kids don't even tell mom or dad," said Allen.