Brandon Toseland, 35, faces a murder charge and two counts of first-degree kidnapping.
Authorities in Las Vegas, Nevada learned of the crime on Tuesday after the boy's older sister handed a note to her teacher. Police say it was written by the toddler's mother.
The note said the mom was being held against her will, and she wasn't sure if her son was alive because she hadn't seen him since December.
"The woman told detectives she had undergone abuse by Toseland, and she was not allowed to leave the house alone or enter the garage," police said in a statement.
The prosecutor on the case said that the child's body had been found with obvious physical injuries. An autopsy was being performed to determine the cause of death.
Police believe the young boy's body had been in the freezer since early December.
This story was originally published on ktnv.com.