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There is a new reservation system in effect if your interested in going from Pt. Towsend to Whidbey Island. This wouldn't be needed if you want to visit Port Townsend from the Seattle area, but many people like to make a loop coming over to Whidbey and back thru Deception Pass. This is new as of May, 2008.
You can make reservations by phone -- (888) 808-7977 or (206) 464-6400 between 7 a.m. and 9 p.m -- on the Washington State Ferries website, or at the Port Townsend or Keystone terminal. Reservations can be made on the day of your trip, or they can be made up to a month in advance. Peak sailing times, such as holiday weekends, are likely to fill up fast, so it's best to make your reservation as early as possible.