Sonoma-Marin Area Rail Transit officials are weighing a base fare of between $4 and $5 for rail commuter service when it begins later this year.

In addition to that one-way base fare, riders would be charged as much as $2 to travel into another zone. Last year the SMART board approved a plan to have five zones when it starts service from downtown San Rafael to the Santa Rosa Airport.

As an example, if the board adopts a $4 base fare and $2 zone charge, the maximum a passenger would pay is $12 to pass through all five zones. SMART officials believe the majority of commuters — 61 percent — would pass between two and three zones.

“We want to attract core commuters going to those two to three zones,” said Farhad Mansourian, SMART’s general manager, at a rail agency meeting Wednesday in Petaluma where fares were discussed. “That’s who we need to capture.”

Once service goes from Larkspur to Cloverdale as planned, there would be seven zones. Under the plan there would be two zones in Marin in both the five- and seven-zone configurations, with the border between San Rafael and Novato the demarcation point.

SMART is likely to offer discounts of between 75 cents and $1.50 for passengers using Clipper-enabled North Bay bus systems to get to the train. There would be senior, disabled and youth discounts as well.

The Clipper card system is similar to FasTrak, which allows drivers to pass through Bay Area toll booths without having to stop and hand over cash. Clipper works in much the same manner, with patrons signing up and allowing their credit cards to have bus, ferry or rail fares deducted.

Clipper users can scan or “tag” their cards on a reader. A computer chip inside the card reads the transaction, information is displayed on the screen and a beep sounds to alert the passenger the card has been read. The Clipper system automatically deducts the correct fare and applies any discounts — including transfers — for each trip.

As envisioned, SMART train station platforms would have Clipper vending and loading machines — one of which was unveiled at Wednesday’s meeting — and card readers for passengers. Scanners will be used by SMART employees on trains to make random fare checks to catch any scofflaws who board without using their Clipper card. There will be retail locations in the community where riders can pick up and load Clipper cards.

SMART needs to generate about $5 million in fare revenue based on its assumption of 3,070 daily riders during the work week. The system expects about 300 riders on each weekend day.

SMART officials also want to develop a discounted annual pass to sell to employers, who can then distribute to employees. Under new federal rules that took effect Jan. 1, an employee can use up to $255 a month of their pre-tax income for monthly transit expenses.

Rail officials plan to further discuss fares in the coming days and look to find the right balance between the base and zone fare add-on. Clipper requires that the SMART board submit final fares by June 15 in order for the machines to be ready by the start of passenger service.

“The train has to be affordable,” said Judy Arnold, SMART board chairwoman and a Marin supervisor.

But board member Jim Eddie said there is value in the trains and passengers should be charged for it.

“We don’t want to under-sell our product,” he said.

SMART promises a speedier southbound commute in comparison to Highway 101. From Railroad Square in Santa Rosa to the Marin Civic Center, the rail service will take 49 minutes, compared with 60 to 90 minutes by car. From Railroad Square in Santa Rosa to downtown San Rafael, SMART says the trip will take 55 minutes on rails, compared with a 60- to 100-minute trip on Highway 101.

“How much is your time worth to you?” Mansourian said as fares were discussed. “You could be cutting your commute in half. Do you want to be sipping a latte and doing work, or be on Highway 101?”