Do EPUB highlights sync across devices?

It depends on the platform. Apple Books highlights sync via iCloud across all Apple devices. Kindle highlights sync via Amazon Whispersync across all Kindle devices and apps. Kobo syncs to the Kobo cloud. Cross-platform sync (e.g., Kindle highlights in Apple Books) requires a third-party service like Readwise, which connects multiple platforms and exports to Notion, Obsidian, or Markdown.

How do I export my EPUB highlights?

Kindle: visit read.amazon.com/notebook for your highlights by book, or find My Clippings.txt on your Kindle (USB). Apple Books: use the third-party Highlights app to export. Kobo: connect via USB and query KoboReader.sqlite (Bookmark table), or use Kobo's web interface. Thorium Reader: go to Bookmarks & Annotations panel → Export → downloads W3C Web Annotation JSON.

Are EPUB annotations stored inside the EPUB file?

No — current e-reader platforms store annotations in platform-specific databases (iCloud for Apple Books, Amazon servers for Kindle, KoboReader.sqlite for Kobo). Annotations don't travel with the EPUB file. The W3C EPUB Working Group is developing an embedded annotations standard, but no major platform implements it yet.

What is Readwise and how does it help with EPUB annotations?

Readwise (readwise.io) is a service that aggregates highlights from Kindle, Kobo, Apple Books, Instapaper, Pocket, and more into one place. It exports to Notion, Obsidian, Roam Research, Markdown, and CSV. It also has a spaced repetition feature that resurfaces highlights for review. Pricing is $7.99/month. It's the most practical solution for readers who use multiple platforms.

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.

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.sqlite with any SQLite viewer. Highlights are in the Bookmark table.

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.

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

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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