The reputed boss of a vicious MS-13 faction “ordered a series of murder missions” — including the gruesome slaying of a 16-year-old boy who was stabbed so many times he was nearly decapitated, federal prosecutors charged at the start of his trial Monday.

Melvi Amador-Rios, 32, the alleged leader of the Centrales Locos Salvatruchas clique of MS-13, is accused of calling hits on multiple rivals and suspected snitches — resulting in the grisly stabbing death of Julio Vasquez in 2017.

“As the leader of the clique, the defendant ordered a series of murder missions,” Assistant US Attorney Rafaella Belizaire said during opening statements in Brooklyn federal court.

Vasquez was lured to Alley Pond Park in Queens on May 16, 2017 where members Josue Leiva and Luis Rivas allegedly stabbed him more than 30 times.

“They nearly decapitated him. They did this because their leader – the defendant – ordered them to do it,” Belizaire said.“They stabbed him over and over and over until he was dead.”

Former MS-13 members and associates cooperating with the feds will testify that Amador-Rios — aka “Letal” or “Pinky” — ordered the hit on Vasquez for disobeying the orders to kill, prosecutors said in a February court filing.

Recorded jail calls, social media posts, Facebook messages between MS-13 members and other evidence will also be presented to show Amador-Rios’ standing in the murderous clique, according to the filing.

Earlier in 2017, the feds allege, Amador-Rios had ordered the killings of three members, beginning with one underling whom he believed was associating with a rival gang.

When the gang was unable to track down the mark, Amador-Rios suspected another member of warning his target — and in turn ordered Vasquez to kill the suspected snitch, prosecutors claimed.

But when Vasquez was unsuccessful in carrying out the order, the group began to believe the teen was working with law enforcement — and Amador-Rios allegedly ordered he be killed as well.

A few days later on May 21, Vasquez’ body was discovered by a 52-year-old birdwatcher who stumbled upon the corpse in the park.

Amador-Rios also faces charges over his alleged involvement in the paralysis of a 16-year-old rival in 2016. He’s accused of directing an underling to kill the teen — an apparent member of the rival 18th Street gang — in order to prove his loyalty and move up in the group.

The victim, Louis Serrano, testified briefly Monday, entering the courtroom in a motorized wheelchair.

He recalled how, on the day he was attacked, a man in a van had pulled up to him and asked if he wanted a ride. When he said he preferred walking, three men came out and confronted him about whether he was in the 18th Street gang.

“They started beating me up,” Serrano told jurors, noting the next thing he remembered was waking up in a hospital bed.

Prosecutors say Amador-Rios had directed the low-level member of his crew — called a “chequeo” — to buy a gun from his brother Santos Amador-Rios for the hit.

The underling roped in two other chequeos and the trio confronted their mark in Jamaica, Queens, beating him and shooting him in the head with the gun they got from Santos, the feds alleged.

The threesome attempted to shoot Serrano a second time but the gun jammed — and the victim survived but now lives as a paraplegic, court papers state.

Serrano told jurors that he wasn’t part of the rival gang, but was friends with two members and had flashed the gang sign in pictures with them.

He was hospitalized for nearly nine months following the attempt of his life, which left him with a gunshot wound to his skull that has required four surgeries, the most recent in March, Serrano said, adding he lives in constant pain.

Belizaire told jurors MS-13 had two rules: To kill rivals whenever possible, and to never snitch to law enforcement. 

A “surefire way” for members to rise up in the notorious brutal gang was by “murdering an enemy,” the prosecutor said.

Amador-Rios’ defense attorney Murray Singer didn’t dispute that his client was a member of the gang — which has spread violence on Long Island in recent years — but told jurors, “It’s not a crime to be affiliated with MS-13.”

“It’s not enough to prove the crimes took place and it’s not enough to prove that Melvi was part of the organization,” he argued. “Melvi’s position… and the defense’s position is he didn’t do these things — he wasn’t involved.”

Amador-Rios faces charges of racketeering, murder in-aid-of racketeering and related crimes. He is also charged for the armed robberies of a money transfer business and three convenience stores in Queens.

Three underlings have pleaded guilty to attempted murder and racketeering for the October 2016 attempted hit on Serrano. Four others have also pleaded guilty in the case — including Leiva and Rivas — for Vasquez’ murder.

Jurors will remain anonymous for Amador-Rios’ trial, which is expected to last two weeks.

He faces mandatory life in prison if convicted of murder.