A $2 billion project to electrify Caltrain — which shuttles 65,000 Bay Area commuters daily — could come to a screeching halt just before construction begins as California’s Republicans in Congress wage a fight over a more controversial project: the state’s effort to link the Bay Area to Los Angeles by high-speed rail.

The project to modernize the Bay Area train line has become an unlikely target of the GOP’s California delegation as it moves to stop California’s bullet train, which would run over the same track. The high-speed rail authority has invested over $700 million in the electrification project.

All 14 members have asked the Trump administration to block a $650 million federal grant slated for Caltrain’s electrification — a move that supporters say would cost thousands of jobs and stall desperately needed fixes to the system.

The maneuver, first reported this week, comes as California braces for retribution from President Donald Trump, who has threatened to pull federal funding from UC Berkeley and the entire state over policy disputes.

Worried that the Caltrain project more than 15 years in the making might fall apart, San Jose Mayor Sam Liccardo and other Silicon Valley leaders say they are working around the clock to persuade GOP representatives and others about what is at stake: a cleaner, quieter train system with more room for the riders who squeeze themselves into its aging diesel cars every day.

“We can’t drop the ball on the final yard line,” said Carl Guardino, president and CEO of the Silicon Valley Leadership Group, a trade association representing 400 employers. “That’s going to only hurt Silicon Valley workers, our economy and our companies, because that’s what this would do.”

Its advocates say that members of Congress are unfairly connecting the two projects — one to electrify Caltrain and the other to build a bullet train from San Francisco to Los Angeles — and treating them as one. Caltrain and its advocates say their project has been in the works for years before the state pursued high-speed rail. The first electric trains are slated to start running by 2021.

“There is a distinction between a train built during the tenure of President Lincoln and one that hasn’t been built,” Liccardo said, “and we hope the Congress will appreciate that distinction.”

Asked why California’s own representatives would try to block funding from the state, Congressman Tom McClintock, R-Roseville, responded with an email about high-speed rail, not the Caltrain project.

“This has never made any sense,” he said, referring to high-speed rail. “I have never supported a dollar of state funding going for this project, and would never support a dollar of federal funding.”

Republican Congressman Jeff Denham, R-Modesto, says the projects are closely intertwined. The Bay Area project, he argues, is also counting on $700 million in state funds from the California High-Speed Rail Authority — bond money that California voters approved in 2008 for high-speed rail.

Denham — who predicts the bullet train will never be completed — calls it “a money grab.”

“I believe in trust in government, and I believe the California state government ought to live up to what it promised voters,” he said.

As a contender for the $647 million federal grant, the Caltrain project underwent a two-year review, receiving “medium-high ratings” from the Federal Transit Administration. It now needs the signature of the new Secretary of Transportation Elaine Chao — typically a pro-forma step done after a 30-day comment period, which ends in mid-February.

But on Jan. 24, just days after President Trump took office, California’s GOP delegation wrote a letter to Chao asking her not to approve the loan and calling for an audit of the bullet train.

California’s Democratic delegation responded with its own letter last week, urging Chao to give her approval. The electrification project, they argued, would create 9,600 jobs, including 1,300 outside of California.

“President Trump recently spoke about infrastructure investment stating that ‘We’ll fix our existing product before we build anything new. We will fix it first because we have a lot of things that are in bad shape,’” they wrote. “We share the commitment of the Administration to upgrade infrastructure that is in disrepair.”

Caltrain spokeswoman Tasha Bartholomew says the funds are needed by March 1. Otherwise, she said, it “would result in delays that could threaten the viability of the electrification project.”

Killing or delaying Caltrain electrification would also undermine California’s bullet train project, as the future high-speed bullet trains would need electrified rails.

In a statement provided to this newspaper, House Minority Leader Nancy Pelosi took sharp aim at her California counterparts.

“If California Republicans derail the Caltrain upgrade, they will kill over 9,600 jobs and will be to blame for dirtier, slower, and more crowded commutes between San Francisco and Silicon Valley,” said a statement from her spokesman Jorge Aguilar. “While Kevin McCarthy is fundraising in Silicon Valley this week, perhaps he can explain to the contributors why he is fighting to make congestion worse along this key innovation corridor.”

Read California House Democrats’ letter to Transportation Secretary Elaine Chao.

Read California House Republicans’ letter to Transportation Secretary Elaine Chao.