EPUB Annotations and Highlights — How They Work Across E-Readers
Highlights, notes, and bookmarks in EPUBs are stored differently on each platform. Here's how annotations work in Apple Books, Kindle, Kobo, and open EPUB readers — and how to export them.
How EPUB Annotations Work
EPUB 3 defines an annotation standard (Web Annotations / EPUB CFI), but most e-reader platforms use proprietary annotation systems. When you highlight text, the reader stores:
- The text content of the highlight
- A location reference (EPUB CFI — Canonical Fragment Identifier — or a page/position offset)
- The highlight color and any attached note
- A timestamp
These annotations are usually stored in the reading app's database, not inside the EPUB file itself. This means annotations don't travel with the file when you copy it to another device or app.
Apple Books Annotations
Apple Books stores annotations in iCloud and syncs across all Apple devices with the same Apple ID:
- Highlight: Select text → tap the highlight color in the popup menu.
- Note: Select text → tap Note → type your note.
- Bookmark: Tap the bookmark icon at top-right of any page.
Export: Apple Books has no built-in annotation export. Third-party apps like Highlights (highlightsapp.net) can extract annotations from Apple Books into Markdown, PDF, or Obsidian format.
Kindle Annotations
Kindle stores annotations in the cloud and in a My Clippings.txt file on the device:
- Highlights, notes, and bookmarks sync via Amazon's Whispersync to all Kindle apps and devices.
My Clippings.txt(found in the Documents folder when Kindle is connected via USB) contains all highlights as plain text.- Online: read.amazon.com/notebook shows all your Kindle highlights organized by book.
- Kindle annotates its converted copy of a sideloaded EPUB, not the original file, so the highlights stay inside the Kindle ecosystem.
Export: The Kindle notebook (read.amazon.com/notebook) lets you export highlights to Notion, or copy them. The clippings file is plain text and easy to parse. Third-party tools like Readwise can sync Kindle highlights automatically.
Kobo Annotations
Kobo stores annotations locally on the device in an SQLite database (KoboReader.sqlite) and syncs to the Kobo cloud (kobo.com/en/p/koboplus):
- Highlights and notes are accessible via the Kobo website at kobo.com → Shelf → select book → View highlights.
- For local access, connect the Kobo via USB and open
KoboReader.sqlitewith any SQLite viewer. Highlights are in theBookmarktable. - Colour highlights are available on the Libra Colour and Clara Colour; other Kobo models use a single highlight style.
Export: Kobo doesn't have a built-in export feature. Use the SQLite database method or the Kobo Highlights Exporter web tool for CSV/Markdown export.
Thorium Reader Annotations
Thorium Reader supports annotations following the W3C Web Annotations spec and can export them as JSON:
- Highlight text → color picker appears → add optional note.
- Go to Bookmarks & Annotations panel → click Export to download a JSON file.
- The JSON follows the W3C Web Annotation Data Model — portable across systems that support the standard.
- Bookmark the current position with Ctrl+B (Windows/Linux) or Cmd+B (Mac). The whole annotation system is keyboard and screen-reader accessible — rare among EPUB readers.
Moon+ Reader and Calibre Annotations
Moon+ Reader (Android): long-press to highlight in one of five colours and attach a note; bookmark from the toolbar or a configurable volume-button shortcut. The Pro version syncs annotations via Google Drive or Dropbox; the free version stores them locally. Export from the reading menu → Share → Export Annotations as plain text with chapter references.
Calibre viewer: highlights and notes are stored in the Calibre library database and can be exported per book from the book details panel — the most convenient built-in export among desktop readers.
Readwise — Cross-Platform Annotation Sync
Readwise (readwise.io) is the most popular third-party service for syncing and exporting reading highlights across platforms:
- Syncs highlights from Kindle, Kobo, Apple Books, Instapaper, Pocket, and more
- Exports to Notion, Obsidian, Roam Research, Markdown, CSV
- Spaced repetition review of highlights
- Pricing: $7.99/month or $79.99/year
Which Reader for Serious Annotation Work?
On the desktop, Thorium Reader (accessible, standards-based JSON export) or Calibre (easy per-book export). On mobile, Kindle has the best built-in export through the web notebook, Kobo works best paired with Readwise, and on iOS Apple Books plus Readwise or the Highlights app is the practical combination. Whatever you choose, highlighting only works if the EPUB contains real text — a PDF converted with OCR or text extraction highlights fine; one converted to page images does not.
Storing Annotations Inside the EPUB File
The EPUB 3 annotations specification (under development by the W3C EPUB Working Group) defines a standard for embedding annotations inside EPUB files. When finalized, it will allow annotations to travel with the file. For now, no major e-reader platform reads or writes annotations embedded in EPUB files — all annotations remain in platform-specific datastores.
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