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Had a look at the FAQ's for both pages and it seems that webapps is more for users of web applications while webmasters is for those who operate websites.

Webapps http://webapps.stackexchange.com/faq

What kind of questions can I ask here?

Web Apps - Stack Exchange is for expert and advanced users of web applications. If your question generally covers …

1. Using Gmail, Facebook, Twitter, Google, or any other website which behaves like an application
2. Bookmarklets
3. Browsers and their features relating to the use of a web application (Greasemonkey scripts for a web application, etc)

Webmasters https://webmasters.stackexchange.com/faq

What kind of questions can I ask here?

Pro Webmasters - Stack Exchange is for professional and enthusiast webmasters. If your question generally covers the operation of websites which you control, then you’re in the right place to ask your question!

Had a look at the FAQ's for both pages and it seems that webapps is more for users of web applications while webmasters is for those who operate websites.

Webapps https://webapps.stackexchange.com/faq

What kind of questions can I ask here?

Web Apps - Stack Exchange is for expert and advanced users of web applications. If your question generally covers …

1. Using Gmail, Facebook, Twitter, Google, or any other website which behaves like an application
2. Bookmarklets
3. Browsers and their features relating to the use of a web application (Greasemonkey scripts for a web application, etc)

Webmasters https://webmasters.stackexchange.com/faq

What kind of questions can I ask here?

Pro Webmasters - Stack Exchange is for professional and enthusiast webmasters. If your question generally covers the operation of websites which you control, then you’re in the right place to ask your question!

Had a look at the FAQ's for both pages and it seems that webapps is more for users of web applications while webmasters is for those who operate websites.

Webapps http://webapps.stackexchange.com/faq

What kind of questions can I ask here?

Web Apps - Stack Exchange is for expert and advanced users of web applications. If your question generally covers …

1. Using Gmail, Facebook, Twitter, Google, or any other website which behaves like an application
2. Bookmarklets
3. Browsers and their features relating to the use of a web application (Greasemonkey scripts for a web application, etc)

Webmasters http://webmasters.stackexchange.com/faq

What kind of questions can I ask here?

Pro Webmasters - Stack Exchange is for professional and enthusiast webmasters. If your question generally covers the operation of websites which you control, then you’re in the right place to ask your question!

Had a look at the FAQ's for both pages and it seems that webapps is more for users of web applications while webmasters is for those who operate websites.

Webapps http://webapps.stackexchange.com/faq

What kind of questions can I ask here?

Web Apps - Stack Exchange is for expert and advanced users of web applications. If your question generally covers …

1. Using Gmail, Facebook, Twitter, Google, or any other website which behaves like an application
2. Bookmarklets
3. Browsers and their features relating to the use of a web application (Greasemonkey scripts for a web application, etc)

Webmasters https://webmasters.stackexchange.com/faq

What kind of questions can I ask here?

Pro Webmasters - Stack Exchange is for professional and enthusiast webmasters. If your question generally covers the operation of websites which you control, then you’re in the right place to ask your question!

Had a look at the FAQ's for both pages and it seems that webapps is more for web applications while webmasters is for general web questions.

Webapps

What kind of questions can I ask here?

Web Apps - Stack Exchange is for expert and advanced users of web applications. If your question generally covers …

1. Using Gmail, Facebook, Twitter, Google, or any other website which behaves like an application
2. Bookmarklets
3. Browsers and their features relating to the use of a web application (Greasemonkey scripts for a web application, etc)

Webmasters:

What kind of questions can I ask here?

Pro Webmasters - Stack Exchange is for professional and enthusiast webmasters. If your question generally covers the operation of websites which you control, then you’re in the right place to ask your question!

Had a look at the FAQ's for both pages and it seems that webapps is more for users of web applications while webmasters is for those who operate websites.

Webapps http://webapps.stackexchange.com/faq

What kind of questions can I ask here?

Web Apps - Stack Exchange is for expert and advanced users of web applications. If your question generally covers …

1. Using Gmail, Facebook, Twitter, Google, or any other website which behaves like an application
2. Bookmarklets
3. Browsers and their features relating to the use of a web application (Greasemonkey scripts for a web application, etc)

Webmasters http://webmasters.stackexchange.com/faq

What kind of questions can I ask here?

Pro Webmasters - Stack Exchange is for professional and enthusiast webmasters. If your question generally covers the operation of websites which you control, then you’re in the right place to ask your question!