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I am currently using Google webmaster tools. I submitted my sitemap using their tool, etc. I am aware of the fact that Yahoo and Bing offer theit own webmaster tools section.

Can I use all three sites' tools or should I pick one of them and stick with it?

Do not know if there is any kind of penalty for using many tools?

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You can use all three tools without penalty or issue. There's absolutely no reason for a search engine to levy a penalty on a website that uses tools that has no direct effect on the website itself (i.e. these tools aren't altering your code or using "techniques" to manipulate the search results). These tools are just informative. Nothing nefarious about them.

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Not only can you, but it's my opinion that you should. Each of them offer their own variation of information. The biggest benefit is you'll be aware of any problems with a particular search engine by using all three (i.e. maybe Bing encounters an error crawling your website, but Y! & GG don't). The exception being that Yahoo! has switched to Bing search results, but their crawler is still chugging along.

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I would not! Doing those kind of choors takes an incredible amount of time. I would do it only for Google and maybe Yahoo. I would not waste a 1 sec on Bing, no traffic comes from it at all, at least when I look at statistics on many different of my cutsomers' sites. –  Marco Demaio Nov 23 '10 at 21:44
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Bing has a large search share, by some measures even bigger than Yahoo's ( searchengineland.com/… ). If you're not seeing very much traffic from Bing, then you either aren't ranking well or are not even in their index. Submitting to their webmaster console might help that. It only takes about 5-10 minutes to do it. –  Matthias Dec 3 '10 at 17:05
    
Things changed since december 2010. Is it still worth to submit a website to the Bing Webmaster Tools? –  waanders May 3 '12 at 12:16
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I asked a while ago if it was ok to have multiple accounts of the same "brand" of webmasters tools (i.e. 2 google accounts on one website - one for me one for an SEO company brought in) and it was ok.

I personally only use google - which generates 80% of our traffic. But I can't imagine a situation where using yahoo/bing/google on the same website will cause any problems.

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Just an FYI reasonably recently Google has added the ability to add owners to your GWT account so you no longer need 2 accounts (although having 2 accounts shouldn't hurt anything). –  Joshak Nov 22 '10 at 13:51
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