The boys' mother told the Los Angeles Times newspaper that the aide, a woman in her 50s, sent at least three letters to her son in 2009, including one that read: "when you get close to me, even if you give me the chills I like that. Don't tell nobody about this!"
The allegations come as school district administrators move to replace the entire staff at Miramonte Elementary School while the Los Angeles Unified School District investigates two teachers arrested last week.
Mark Berndt, 61, is charged with committing lewd acts on children, ages 6 to 10, between 2005 and 2010. The alleged acts include blindfolding children, feeding them semen, taping their mouths and photographing them in a "game." Berndt was fired in January 2011.
The furor led to two parents coming forward to complain that teacher Martin Springer, 49, fondled two second-grade girls in his classroom. The school board on Tuesday voted unanimously to fire Springer.
Police have set forth no connection between the cases, but parents' confidence has been badly shaken.
In the latest allegations, the teacher's aide wrote a letter signing herself "sad girl" because she was being transferred to another school, the mother alleged.
The mother went to the Los Angeles County Sheriff's Department, which directed her to the school. During a meeting that included the mother, her son, his teacher and an assistant principal, the teacher's aide acknowledged writing letters and said she had a grandmotherly affection for the boy.
The aide no longer works for the school system, district spokeswoman Gayle Pollard-Terry said.
All 120 staff members at Miramonte will be replaced as of Thursday.
"It's the most severe action I've seen taken by a school district," said Terri Miller, president of Stop Educator Sexual Abuse, Misconduct and Exploitation, an advocacy organization based in Las Vegas.
The decision Monday came after about three dozen people protested in front of the main doors of the school earlier in the day, some carrying a banner that read, "We the parents demand our children be protected from lewd teacher acts."
School sex abuse expert Mary Jo McGrath, an attorney who has conducted some 350 abuse investigations, said the investigation could uncover more cases.
"It's not a witch hunt, it's just that someone is really looking," she said. "Cases start unpeeling like an onion. It's always the same pattern."
Associated Press writer Robert Jablon contributed to this report.