Victoria Marquina was 16 years old and pregnant when her mother reported her missing at Sutter Creek in October 2019.
Nearly six years later, Joshua Martinez was charged with murder.
Investigators said they had a short relationship, in which Martinez was 21 years old at the time.
"Martinez faces a maximum sentence of life in prison." San Joaquin District Attorney Ron Freitas said.
The district attorney worked with multiple agencies as part of a cold case task force.
When asked why it took six years to file charges, Freitas said:
"That's a very good question and we aren't going to get into specifics at this time. So much of this is just dogged tirelessness of our investigation, dotting every 'i' and crossing every 't.'"
Although a suspect has been charged with her murder, Marquina's body still has not been found.
"We want to bring closure to Victoria's mother and allow her to bury her child and her grandchild," the district attorney said.