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On my account page, I see Hacker account can have "web app on your own domain" while web dev can have "web apps on custom domain" so I wonder what's the difference between "your own domain" and "custom domain". In other words, I want to set my app on my custom domain which is www.mydomain.com. Can I do this with hacker account (This guide says free and hacker accounts can't do this)?

Sorry about that, we should be more consistent about the wording. We mean the same thing when we say "own domain" or "custom domain", we're trying to say "any domain that doesn't end in .pythonanywhere.com", or "a domain you've registered yourself".

That guide is out of date -- will fix it. The reason is that, until recently, hacker plans didn't support own-domains. But now they do.