When comparing Windows Subsystem for Linux vs MobaXterm, the Slant community recommends Windows Subsystem for Linux for most people. In the question“What are the best collections of Unix libraries for Windows?” Windows Subsystem for Linux is ranked 1st while MobaXterm is ranked 6th. The most important reason people chose Windows Subsystem for Linux is:
There's no VM overhead because WSL is not a VM.
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Pros
Pro Light resource usage unlike virtual machines
There's no VM overhead because WSL is not a VM.
Pro Includes common UNIX utilities
Windows Subsystem for Linux comes with common UNIX utilities such as grep
, awk
, etc.
Pro Supports multiple Linux distributions
WSL supports multiple Linux distros, and you can use the distro's package manager (e.g. apt-get
on Ubuntu) to install other tools and binaries.
Pro Runs native Linux tools
Pro Flexible
MobaXterm can connect to practically anything.
Pro X server support
In case you need X11 forwarding, MobaXterm has an integrated X server.

Pro Full linux subsystem with package manager
And you can install conda for additional package management.
Pro Tabbed or split mode
Multiple terminals can either be in tabs or split horizontally or vertically.

Pro Integral remote file editor
Edit remote files via ssh and sftp
Pro SSH tunnel controls and forwarding UI controls makes it easy
Pro Automatic SFTP
With MobaXterm, there's no fiddling with multiple apps: simply connect and everything is available.
Pro Connection manager
Pro ENV can use Windows PATH
Pro Password vault
Pro Server tools (HTTPD, SSHD, SFTPD, TTFT)

Pro Build in sftp file manager
Manipulate and edit remote files in the file browser.

Pro Integrates with WSL
Integrates perfectly with the Windows Subsystem for Linux. Out of the box it offers a shell to that system.
Pro Supports macro controls (multi commands in single screen)
Cons
Con Too complicated
It's complicated to use as it requires moving files to/from wsl to base windows.
Con You can't mix and match installations - utilities added to the subsystem are only available in the subsystem
If you install node in the Windows subsystem, it is not available in Windows, only in the subsystem and vice versa.
Con Not completely freeware
If you use MobaXterm at work, they hope you will pay for it. This isn't horrifying, but it's not providing any new features in Linux to warrant the outlay. Its integration with Putty in Windows as an X client may make it worth the funds.
Con Split screen prevents tabbed mode
If you split a screen within a tab, you have to go back to single screen before you can switch to another tab.
Con Can have some performance issues
MobaXterm can have some occasional performance issues. These happen rarely but it's worth mentioning that they exist, especially since this is a paid tool.
