How to Use Bookmarks and Highlights in EPUB Readers (2026 Guide)

June 12, 2026  ·  7 min read

Annotations — bookmarks, highlights, and notes — are one of the primary reasons readers prefer a dedicated EPUB app over a basic viewer. This guide covers how each major platform handles annotations and how to export or back them up.

Apple Books

Highlights: Tap and hold to select text → choose a highlight color (yellow, green, blue, pink, purple) or underline. Notes can be attached to any highlight.

Bookmarks: Tap the bookmark icon in the top-right corner to bookmark the current page. Access all bookmarks in the Notes panel (tap the speech bubble icon).

Sync: All highlights, notes, and bookmarks sync across iPhone, iPad, and Mac via iCloud automatically. No setup required.

Export: No native export in the current version. Third-party tools like Readwise can sync Apple Books highlights via clipboard. For manual export, highlights are stored in a SQLite database at ~/Library/Containers/com.apple.BKAgentService/Data/Documents/iBooks/Books/ on Mac — accessible with a SQLite browser.

Limitation: Highlights are tied to your Apple ID and do not travel with the EPUB file itself. Moving to a different reading app loses the annotations.

Kindle

Highlights: Tap and hold on a word → drag to extend selection → tap Highlight. Choose from four colors. Add a note by tapping the Note icon on the highlight toolbar.

Bookmarks: Tap the top-right corner while reading to add a bookmark. Access via the toolbar menu → Bookmarks.

Sync: Whispersync syncs highlights, bookmarks, and reading position across all Kindle devices and apps tied to your Amazon account.

Export: All highlights are accessible at read.amazon.com/kp/notebook — browse by book, copy individual highlights, or export all highlights for a book as plain text.

Note: Kindle handles EPUB only after conversion to Kindle format. Annotations are on the converted file, not the original EPUB.

Kobo

Highlights: Tap and hold text → drag to select → tap Highlight. Kobo e-ink devices offer color highlighting on the Libra Colour and Clara Colour; other models use a single highlight style.

Bookmarks: Tap the top-right corner to bookmark. View all bookmarks from the reading menu.

Sync: Kobo syncs annotations to your Kobo account if you're signed in. The Kobo app (iOS/Android) shares the same sync.

Export: Kobo stores annotations in a SQLite database (KoboReader.sqlite) on the device — accessible when connected via USB. Tools like Kobo Highlights Exporter read this database and export to Markdown or CSV. Readwise also supports Kobo sync via a direct integration.

Thorium Reader

Highlights: Select text → right-click → Highlight (or use the toolbar). Supports multiple colors.

Bookmarks: Keyboard shortcut Ctrl+B (Windows/Linux) or Cmd+B (Mac) adds a bookmark at the current position. View all bookmarks in the navigation panel.

Annotations panel: All highlights and notes are listed in the Annotations panel, accessible from the sidebar. Supports filtering by color.

Export: Thorium stores annotations in a local JSON database. As of 2026, there is no one-click export, but the database is human-readable and accessible for scripting.

Accessibility: Thorium's annotation system is fully keyboard and screen reader accessible — unlike most other EPUB readers.

Moon+ Reader (Android)

Highlights: Long-press text → drag → tap Highlight. Five colors available. Notes can be added to any highlight.

Bookmarks: Tap the bookmark icon or use the volume button shortcut (configurable). Access via the bookmarks panel in the reading menu.

Sync: Moon+ Pro syncs annotations via Google Drive, Dropbox, or local backup. Free version stores annotations locally only.

Export: Moon+ can export highlights to a text file from the reading menu → Share → Export Annotations. Format is plain text with chapter references.

Exporting and backing up annotations

Annotations are one of the biggest pain points when switching EPUB readers — most stores lock annotations to their own formats. Options:

• Readwise: Aggregates highlights from Kindle, Kobo, Apple Books, Instapaper, and more into a single searchable database. Exports to Markdown, Notion, Obsidian, Roam, and others. Paid service ($7.99/month).
• Manual SQLite access: Kobo and Calibre both store annotations in SQLite databases that you can query directly.
• Calibre annotations: If you read via Calibre's viewer, annotations are stored in Calibre's library database and can be exported per-book via the book details panel.
• EPUB annotations standard: The W3C Web Annotation standard allows annotations to be stored in the EPUB file itself (in a separate JSON file). Very few readers implement this yet — it's a future standard, not current practice.

FAQ

Do highlights travel with an EPUB file if I move it to another app?

Generally no — most reading apps store annotations in their own database, not in the EPUB file itself. Moving an EPUB to a different app means starting fresh with annotations. Readwise is the best tool for aggregating highlights across apps.

Can I highlight text in a converted PDF-to-EPUB?

Yes, if the conversion preserved real text (not images). EPUBs from toolkit.bot contain real, selectable text — highlighting works in all the apps above. Scanned PDFs that were OCR-processed also produce selectable text in the output EPUB.

What is the best EPUB reader for serious annotation workflows?

For desktop: Thorium Reader (full keyboard + screen reader support) or Calibre (good annotation export). For mobile: Kindle (best export via the web notebook) or Kobo (best with Readwise integration). For iOS: Apple Books + Readwise for export.