How to Compare Two Folders in Linux

Every command below is part of a standard Linux install (GNU diffutils, coreutils, rsync) and works the same way on Ubuntu, Debian, Fedora, Arch, and in WSL. The example output comes from two test folders, dir1 and dir2, where b.txt has different content and each side has one file the other lacks.

Method 1: diff -rq (the Standard Way)

$ diff -rq dir1 dir2
Files dir1/b.txt and dir2/b.txt differ
Only in dir1/sub: only1.txt
Only in dir2/sub: only2.txt

• -r recurses into subdirectories.
• -q reports only whether files differ. Leave it out and diff prints every changed line inside every text file, which is useful for two copies of a source tree and overwhelming for anything else.
• Only in dir1/sub: only1.txt means the file exists only on that side.
• No output and exit code 0 means the folders match. Exit code 1 means differences were found, so diff -rq a b >/dev/null && echo same works in scripts.

Useful flags

# Also list files that are identical
diff -rqs dir1 dir2

# Skip folders and file types
diff -rq --exclude=".git" --exclude="*.log" dir1 dir2

# Treat a missing file as empty: reported as "differ" instead of "Only in"
diff -rqN dir1 dir2

Method 2: Compare File Lists Only

On very large trees, reading every byte is slow. If you only need to know which files are missing, compare the file lists with find and comm (Bash or zsh):

$ comm -3 <(cd dir1 && find . -type f | sort) <(cd dir2 && find . -type f | sort)
./sub/only1.txt
	./sub/only2.txt

The first column lists files only in dir1; the tab-indented second column lists files only in dir2. Use comm -23 to print just the first column (files missing from dir2). This finishes in seconds even on millions of files, but it cannot tell you whether a file present in both folders has changed.

Method 3: Compare by SHA-256 Checksum

Checksums are the most reliable way to prove that two folders hold the same data, and the list you create doubles as a record you can check again later. Build a sorted SHA-256 list for each folder and diff them:

(cd dir1 && find . -type f -exec sha256sum {} + | sort -k2) > dir1.sha256
(cd dir2 && find . -type f -exec sha256sum {} + | sort -k2) > dir2.sha256
diff dir1.sha256 dir2.sha256

Any line that appears on only one side is a missing file or a file whose hash changed. Because the paths are relative (./b.txt), the two lists can come from different machines: run the first line on the old server and the second on the new one, then copy one file across.

To check a copy directly against the saved list, run sha256sum in verify mode inside the copy:

$ cd dir2 && sha256sum -c --quiet ../dir1.sha256
./b.txt: FAILED
sha256sum: ./sub/only1.txt: No such file or directory
./sub/only1.txt: FAILED open or read

--quiet hides the OK lines, so only problems are printed. This direction finds files missing from or changed in the copy, but not extra files added to it. Our sha256sum verification guide covers the checksum format and common errors in more detail.

Method 4: rsync Dry Run (Best for Remote Folders)

rsync is normally a copy tool, but with -n (dry run) it only reports what it would do, which makes it a fast directory comparison that also works over SSH:

# Local folders
rsync -rcni --delete dir1/ dir2/

# Local folder vs a folder on another server
rsync -rcni --delete dir1/ user@server:/srv/dir2/

• -n is the dry run. Never drop it while comparing: with --delete, a real run removes files from dir2.
• -c compares contents by checksum instead of size and modification time.
• -i itemizes each difference: >f+++++++++ is a file only in dir1, >fc is a file whose content differs, and *deleting is a file only in dir2.
• Keep the trailing slash on dir1/. Without it, rsync compares dir1 as a subfolder inside dir2 and reports everything as new.
• Add -t or -p to also flag different timestamps or permissions.

GUI: Meld and KDiff3

For a visual comparison, Meld is the usual choice on GNOME-based desktops. Install it from your package manager (sudo apt install meld or sudo dnf install meld) and run meld dir1 dir2. It shows both trees side by side, colors missing and changed files, and lets you open any changed text file in a line diff. KDiff3 offers a similar directory view and fits KDE desktops. Both are free.

No desktop, or comparing a folder you copied from Windows or a Mac? The free Folder Compare tool runs in any browser: upload two folders (up to 100 files and 50 MB each) and it hashes them in memory on our server, without storing them, and lists missing, added, and changed files.

Repeatable Checks and Reports

The commands above answer “are these two folders the same right now?” They get awkward when you need to check the same folders every week, share the result with someone who doesn't use a terminal, or keep proof that a migration was complete before deleting the source.

FolderManifest does this as a desktop app for Linux, Windows 10/11, and macOS. It compares two folders by SHA-256, saves a folder manifest (every file with its path, size, dates, and hash), and exports the result as an HTML, CSV, or Markdown report. Its command-line interface ships inside the Linux app, so the same check can run from cron:

foldermanifest compare-folders /mnt/old-nas/projects /srv/projects

Like diff, it exits with code 1 when the folders differ, so scripts can alert on drift. Files are read locally and never uploaded. See the CLI documentation for every command, or our guides to comparing folders on Windows and on a Mac.

Frequently Asked Questions

Continue Learning

• Verify Checksums on Linux with sha256sum →
• How to Compare Binary Files →
• Compare Two Folders on Windows →