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I've tried to do two kinds of searches which I had previously thought were a source of the same data, but are apparently different.

The first is doing a google search that looks like link:http://mydomain.com which I assumed returned all of the links indexed by Google Crawler which linked to my page:

Google external link search

The second is within Webmaster Tools in the Links to Your Site functionality:

Webmaster Tools External Links

The reason I'm confused by this is that it appears that there don't seem to be as many in-bound links appearing in the link: google search as there are appearing in the Links on Your Site functionality in Webmaster Tools, so it seems to me that these two functions are not referring to the same data as I previously assumed.

If this is not the case, then what are each of these referring to?

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up vote 2 down vote accepted

They're basically both from the "same data." Google reveals what Google reveals, which in general, seems to be some links publicly for anyone to see and more links privately for those who have confirmed they have access to the site. Google doesn't even reveal every link it knows about to webmasters; it's all a combination of choice and physical limitations. Here Matt Cutts explains some of the different limitations and reasons for those limitations.

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