SAN DIEGO — When President Donald Trump came back into office in January, his administration immediately directed federal prosecutors across the country to charge potential criminal defendants with the most serious provable crimes, placing a special emphasis on immigration-related prosecutions.

“The Department of Justice shall use all available criminal statutes to combat the flood of illegal immigration that took place over the last four years,” Attorney General Pam Bondi wrote in a memo to federal prosecutors shortly after she was sworn in.

Since that time, the U.S. Attorney’s Office for the Southern District of California, which covers San Diego and Imperial counties, appears to be faithfully carrying out the administration’s directives. At a time when immigrant apprehensions along the border have plummeted, federal criminal prosecutions of undocumented border-crossers in the San Diego and Imperial Valley region have spiked, according to data from the U.S. Attorney’s Office and U.S. Customs and Border Protection.

“The Department of Justice’s guidance from January and February 2025 contributed to a remarkable achievement — the securing of the border,” the U.S. Attorney’s Office for the Southern District of California said in a statement. “Encounters reaching historic lows demonstrate the powerful deterrent effect of increased criminal prosecutions on those who would consider attempting to illegally enter the country.”

The decrease in immigrant apprehensions at ports of entry and areas in between by Border Patrol agents and customs officers began last year when President Joe Biden enacted stricter asylum restrictions, but those encounters fell at an even higher rate when Trump took office.

Meanwhile, the increase in prosecutions and the directives from DOJ to charge more individuals with immigration offenses is reminiscent of Trump’s first term, when he enacted a zero-tolerance policy aimed at criminally charging all undocumented immigrants.

Though total prosecution numbers were much higher during Trump’s first term because of increased apprehensions, a recent report from Syracuse University’s Transactional Records Access Clearinghouse found that the proportion of people being charged criminally after they’re apprehended at the border is higher now than even during the height of “zero tolerance.”

“The administration considers this to be a top priority, so this is the result — huge numbers of prosecutions,” said David Bier, the director of immigration studies and the Selz Foundation chair in immigration policy at the Cato Institute, a libertarian think tank.

Tom Wong, an associate professor of political science at UC San Diego and the founding director of the university’s U.S. Immigration Policy Center, said the administration’s immigration policies have been successful at fulfilling their intended purposes — for now, at least. But he said immigration patterns and policies can be a “cat and mouse game,” and the reasons for the current decrease in immigration are more complex than just pointing to Trump’s aggressive border policies.

Wong also said the decision for immigrants to try to come to the U.S. is influenced by a number of social factors — and the threat of criminal prosecution or conviction is a deterrent to some, but not to all.

“Motivated individuals who are desperate to reunite with family members, or have no other means of subsistence and are trying to come here to work, will come no matter the circumstances,” Wong said. “Criminal prosecutions … may play a small role in deterring people, but those who are most desperate will try to enter despite the consequences.”

While the national spotlight in recent months has focused on U.S. Immigration and Customs Enforcement and its arrests of undocumented immigrants already living in the U.S., most of those arrests result in civil immigration cases and deportations. The vast majority of criminal immigration-related prosecutions in San Diego remain centered on people caught trying to illegally cross the border.

The data

According to CBP data, Border Patrol agents and customs officers along the California-Mexico border were apprehending an average of more than 33,000 single adults per month between October 2023 and May 2024. That number peaked in April 2024 with 37,898. (The Union-Tribune in its analysis focused only on encounters with what CBP describes as single adults, since they are most likely to face criminal prosecution compared to unaccompanied minors or families.)

During this period under the Biden administration, many people apprehended at the border were seeking asylum and voluntarily presented themselves to Border Patrol agents. Those people were often processed by Border Patrol and then allowed into the country while awaiting immigration proceedings.

In June of last year, in the midst of a re-election campaign struggling to address immigration issues, the Biden administration announced severe restrictions on asylum seekers. By July, apprehensions had dropped below 20,000 per month and continued falling until Trump took office.

Apprehensions fell even further after Trump immediately issued executive orders aimed at curtailing the ability of immigrants to seek asylum. Among those measures was shutting down the CBP One application that had allowed some asylum seekers waiting in Mexico to schedule screening appointments. A lawsuit filed in June in San Diego federal court argued that Trump’s “Asylum Shutdown Policy” is illegal, and his administration must restore the ability for immigrants to seek asylum.

But while that lawsuit and others challenging the administration’s border enforcement policies progress, the directives have had their intended consequences. CBP reported 2,628 apprehensions of single adults along the California-Mexico border in February, Trump’s first full month back in office, down from 10,455 in January. That number was down to 1,452 by July, the most recent month for which there is data available.

In the Southern District of California, which covers the entire California-Mexico border, prosecutions for alleged immigration violations have spiked during the same time period.

In December, Biden’s last full month in office, federal prosecutors in San Diego, then under the leadership of Biden-appointee Tara McGrath, filed 100 cases charging felony re-entry and 27 cases charging misdemeanor illegal entry. By May, under the leadership of Trump-appointee Adam Gordon, those figures had jumped to 331 cases charging felony re-entry and 155 cases charging misdemeanor illegal entry.

At the same time, apprehensions had decreased by 92.6% from the same month the previous year, yet prosecutors filed 353% more illegal re-entry cases.

Though prosecutors are initially charging anyone with a prior deportation or removal with felony re-entry, the majority of those defendants who do not have more serious criminal histories are later pleading guilty to a misdemeanor charge of illegal entry. Attorneys are referring to these as “flip” cases, and judges are sentencing most defendants to time-served custody terms. Those individuals are then quickly deported.

For example, a Mexican citizen was arrested by CBP officers on Aug. 18 after trying to enter the U.S. through the San Ysidro Port of Entry, according to court documents. He told officers that he was a U.S. citizen, but the officers conducted a records check and determined he was not and had previously been deported to Mexico in 1987 and again in 2024.

Prosecutors initially charged him with a felony re-entry count, but about two weeks later charged him with both a felony re-entry count and a misdemeanor illegal entry count. He pleaded guilty to the misdemeanor and was sentenced Tuesday to a term of time served. He was expected to be immediately deported.

Though there’s been a recent spike in such prosecutions since Trump took office, they’re nowhere near the levels seen during “zero tolerance.” For four straight months beginning in July 2018 when that policy was first implemented, federal prosecutors in San Diego filed more than 1,000 immigration-related cases per month, according to data from the U.S. Attorney’s Office.

In August 2018, for example, San Diego federal prosecutors filed 1,101 illegal entry cases and 158 illegal re-entry cases. Compare that to last month, when prosecutors filed 84 illegal entry cases and 161 illegal re-entry cases.

On the other hand, the data show that prosecuting human smuggling cases has remained consistent across multiple administrations.

DOJ directives

The mandate to focus on immigration-related cases came from DOJ’s top leadership immediately after Trump’s inauguration.

On Jan. 21, Trump’s first full day back in office, then-acting Deputy Attorney General Emil Bove sent a memo to all DOJ staff ordering federal prosecutors to “charge and pursue the most serious, readily provable offenses” against all potential defendants — including individuals suspected of illegally crossing the border. It also directed federal prosecutors to “pursue charges relating to criminal immigration-related violations when such violations” are referred by law enforcement.

Bove went on to write that if federal prosecutors declined to prosecute an immigration-related case that was referred to them, they were required to submit an “Urgent Report” to DOJ officials detailing the decision not to pursue the case. According to the section of the Justice Manual cited by Bove, such reports are usually reserved for informing DOJ officials about high-priority and potentially high-profile matters, such as prosecutions of elected officials or political candidates.

On Feb. 5, the day after Bondi was confirmed by the Senate, she sent a follow-up memo reinforcing the directives that Bove had laid out.

“Consistent with the core principle of pursuing the most serious, readily provable offense, U.S. Attorney’s Offices … shall pursue charges relating to criminal immigration-related violations when such violations are presented by federal, state, or local law enforcement or the Intelligence Community,” Bondi wrote.

The July report from Syracuse University’s TRAC found that the decrease in immigrant arrivals and increase in immigration-related prosecutions along the California-Mexico border mirrored what’s happening more broadly in the four other federal districts bordering Mexico.

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