SANTA ROSA (BCN) — A proposed passenger train between Sonoma and Marin counties will initially run between Santa Rosa and San Rafael, not between Cloverdale and Larkspur, the Sonoma Marin Area Rail Transit’s board of directors decided Saturday.

The board voted to initially build and operate only that 40-mile segment between the counties’ two largest cities because of a $350 million funding gap. The funding deficit was $155 million last year.

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The 25 percent funding deficit is due to less revenue from a quarter-cent sales tax in both counties and modifications to the bond market, both of which finance the project, SMART’s general manager Lillian Hames said.

It will cost $395 million to build the segment between Railroad Square in Santa Rosa and the Marin County Civic Center in San Rafael.

That segment would serve 57 percent of the entire 70-mile line’s forecasted ridership between Cloverdale and Larkspur. SMART hopes to have the train running between San Rafael and Santa Rosa in 2014.

Building the segment between Railroad Square and Cloverdale will cost $218 million, and building the Marin Civic Center to Larkspur segment will cost $69 million when more funding becomes available, the board of directors said. The board hopes money will be available between 2016 and 2018.

Ten board members voted to build the Santa Rosa-San Rafael segment first. Director Madeline Kellner of Novato voted not to, and director Judy Arnold, also of Novato, abstained.

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Arnold said Monday morning she wanted to vote yes Saturday but preferred the board postpone its vote until another board meeting Wednesday in San Rafael when Marin County residents can weigh-in on the issue.

Arnold said a final vote will be taken Dec. 15.

The cost of building the entire line and a bicycle and pedestrian path was originally $590 million but has grown to $695 million.

SMART spokesman Chris Coursey said the board members wanted to vote on the issue at the six-hour workshop on six alternative construction scenarios Saturday because all its members were present and only six or seven would be at the meeting Wednesday at the San Rafael City Hall.

The board also wants to solicit construction contracts soon because bids are expected to be low in the still slumping, high unemployment economy, Coursey said.

The contracts include building the rail cars, train stations and more work on the Northwestern Pacific Railroad tracks.

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