A twice-deported illegal immigrant from Mexico was being held Tuesday in the disappearance of a 14-month-old boy who became the subject of an Amber Alert last week after his mother was found dead upstate.

Evarardo Donoteo-Reyes, 25, is currently charged with tampering with evidence, but prosecutors expect to file more charges against him once cops determine how his 18-year-old girlfriend, Selena Hidalgo-Calderon, was killed.

The young woman’s son, Owen Hidalgo-Calderon, is feared dead following an extensive search of the couple’s home in Wayne County and surrounding areas. The toddler was reported missing on May 23 after his mom’s body was discovered near their residence.

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Authorities canceled his Amber Alert on Tuesday morning but continued to look for his body.

Donoteo-Reyes and Hidalgo-Calderon both lived and worked on a 350-acre farm in Sodus, which is located on Joy Road.

Hundreds of volunteers have combed through the property in search of Owen and nearby waterways have also been checked. His mother’s body was found in a wooded area not far from their home — buried between two logs and covered in sticks and dirt, cops said.

Donoteo-Reyes was later arrested at an undisclosed location outside of Wayne County, according to prosecutors.

He appeared in court Tuesday on the tampering with evidence charge, which came after he confessed to moving Hidalgo-Calderon’s body.

Assistant District Attorney Christine Callanan told The Post that Donoteo-Reyes admitted to cops that he buried the young mother, but didn’t kill her. He allegedly did this because he was worried about being deported or blamed for her death.

Prosecutors plan to present his case to the grand jury, but Callanan said they are only focusing on the tampering charge for the time being. Reyes will continue to be held by police in lieu of $25,000 cash bail or $50,000 bond.

According to Immigration and Customs Enforcement, the young man has been living in the United States illegally and using an alias.

“On May 24, ICE lodged a detainer on Everardo Donoteo-Reyes aka Alberto Ebavardo Gutierrez-Reyes, an illegally present citizen of Mexico, with the Wayne County Sheriff’s Office following his arrest on local charges,” the agency said in a statement. “Donoteo-Reyes was removed from the United States on two previous occasions in 2016 and 2017. Donoteo-Reyes has a 2017 federal conviction for illegal entry.”

Selena Hidalgo-Calderon was also an illegal immigrant herself — who was in the process of being deported — but her family has pending applications for asylum. She came to the US from Guatemala and reportedly had her baby with another man, who still lives there.

Wayne County Sheriff Barry Virts told local reporters on Monday that while he hoped Owen was still alive, investigators highly doubted it.

“We have to look to reality here that he is concealed somewhere here on the farm,” Virts said, according to the Rochester Democrat & Chronicle.

“We will bring justice,” he added. “We are going to keep after this until we get the evidence and the information we need.”