This is an extensive of active libraries in the deep web.
Last checked: April 2019

Z-Library

http://loginlibhuwhnmis.onion/
http://zlibraryexau2g3p.onion
The Z-Library is the world’s largest e-book library available. More than 3.4 million books and over 74 million articles for the price of nothing. The Z-Library is also reachable on the clear net via https://b-ok.xyz/. All books and articles are available to registered users, there might be a limit on downloads – approx. 5 downloads per day.

Clockwise Library

http://clockwise3rldkgu.onion/
“Library Clockwise” — About 30,000 books housed in Calibre. Two parts, Arts and Science, lots of academic books, almost all in English.

Anarchist Bookstore

http://b2fxrnttdue72ntq.onion/
Here you will find e-books all around the topics of privacy, security and training. “Car bomb – Recognition Guide” & “How to be invisible” are just two of the books offered. A click on the book cover will lead you directly to the e-book (mostly PDF versions).

Comic Book Library

http://r6rfy5zlifbsiiym.onion/
Yes, finally a large comic book library in this list! The “Comic Book Library” currently contains 1,321 comics, reaching all the way back to 1937.

Guide to an anonymous OS

http://yuxv6qujajqvmypv.onion/
The .onion-site states on their page that this is “A Beginner Friendly Comprehensive Guide to Installing and Using A Safer Anonymous Operating System”. As of right now, you can’t really do much on there since no link redirects you to a library or to the guides. Interesting enough is that they are currently in beta testing (version 1.7.1).

Strategic Intelligence Network

We have not found an active working link yet.

FB2 Library

http://fb2lib3argrtulnw.onion/
The FB2 Library is a Russian online library. It currently provides around 275,000 books, including Russian, German, Italian, English and other book languages.

Flibusta

http://flibustahezeous3.onion/
Flibusta is a Russian library and describes itself as an independent library resource. The library operates on the principle of wiki. This means that the addition of books, authors and any other information is made by users. 
Access via clear net: http://flisland.net/

The Bookshelf

http://savkhz37olwuub37.onion
“The Bookshelf” – Mostly fiction, Russian and English language. Search, or browse by genre, author, rating. Extra functionality for registered users.

Imperial Library of Trantor

http://xfmro77i3lixucja.onion
The Imperial Library currently has close to 300,000 e-books available for users. Most are German, but English, Spanish and Italian books can be found as well.


Link Collections

http://mx7rwxcountermqh.onion/
Above you will find .onion-sites to lists of e-book libraries on the deep web. Most have been checked and are on the page. Happy reading!