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| Alphabetical | By Popularity | | - Bird & Beckett Books
 - Offering an eclectic selection of books and weekly live jazz. - Black Oak Books
- Offers new and used books.
- Books Inc.
- Independent bookseller with locations throughout California.
- Booksmith
- Check out upcoming author readings, featured books, and even meet the staff. Keep your eyes peeled for more exciting features, including exclusive literary journal material and book reviews.
- Borderlands Books
- Specialising in science fiction, fantasy, and horror.
- Builders Booksource
- Books and technical reference for the design and construction industry.
- City Lights Books
- Famed San Francisco bookstore and intellectual Mecca.
- Cover To Cover Books
- An independent bookstore specialising in childrens books and signed editions.
- Eastwind Books & Arts, Inc.
- Founded in 1979 to give its customers access to Chinese and English language publications.
- Get Lost Books
- Find travel books, maps, and gear.
- Jeremy Norman & Co., Inc.
- Offers rare and new books in the history of medicine, science, and technology.
- Last Gasp
- Publishing and distributing underground and alternative books, comics and magazines.
- Limelight Books
- Specialising in theatre and film books.
- Modern Times Bookstore
- Offers collections of cultural theory and alternative and international fiction.
- Omnivore Books on Food
- Sells new, antiquarian, and collectible books on food and drink. Collection includes signed first editions and books dating to the 19th century. Store hosts author and community events.
- San Francisco Mystery Bookstore
- Between Castro and Diamond.
- Stacey's Bookstore
- Specialties include medical, technical, and business books.
- William Stout Architectural Books
- Carries titles in art, furniture and interior design, graphic and industrial design, as well as architecture.
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