SAN DIEGO -- A U.S. Border Patrol agent was in custody Tuesday for allegedly harboring illegal immigrants, including his father, in his San Ysidro home.

Marcos Gerardo Manzano Jr., 26, was arrested Monday at the Imperial Beach Border Patrol Station, according to the FBI.

Shortly before sunrise Tuesday, a federal SWAT team raided Manzano's house in the 3600 block of Shooting Star Drive and arrested suspected undocumented immigrant Jose Alfredo Garrido-Morena, also 26.

People in the normally quiet neighborhood were awoken to the sound of helicopters above and the sight of heavily armed law enforcement on the street.

"I was like, 'What the … is going on?" said longtime neighbor Rick Bush.

Bush proceeded to open his garage door and what he saw was startling.

"There was all kinds of like, [what] looked like military, SWAT and it said FBI on the back and I was like, 'Whoa … something's going on down here,'" he said.

According to a complaint unsealed in U.S. District Court in San Diego Tuesday afternoon, Garrido-Morena had been living at the residence since at least November along with Manzano and the accused agent's 46-year-old father, Marcos Gerardo Manzano Sr.

The elder Manzano, who faces federal immigration-violation charges in the case, remains at large, according to the FBI.

In addition to purportedly harboring undocumented immigrants, Manzano Jr. allegedly lied to a fellow Border Patrol agent when asked while on duty if he knew the whereabouts of his father, who was convicted four years ago in a U.S. court of possessing marijuana for sale and was twice deported to his home country of Mexico.

Manzano Jr. and Garrido-Morena were being held in the Metropolitan Correctional Center in downtown San Diego pending their initial appearances in federal court, scheduled for Wednesday.

10News learned Garrido-Morena has had previous run-ins with the law. According to court documents obtained by 10News, Garrido was arrested in October 2009 on charges of possession of a controlled substance, methamphetamine and for giving false information to a peace officer. The charging document said Garrido-Morena tried to avoid arrest by telling the arresting officer that he was someone else.

Authorities declined to reveal why they felt it necessary to deploy the heavily armed SWAT squad, backed by San Diego police, Customs officers and Border Patrol personnel, to serve the warrant at Manzano Jr.'s home.

During the raid, agents detained a second man and three women for questioning, then released them. A year-old boy also was present during the search, according to the FBI. The relationship of those people to the defendants was unclear.