Google webmaster tools just showed a decrease in my site's backlinks from 1250 to 966. I am bummed...I have been working really hard on getting high quality links for the last couple of months. Has anyone else noticed something similar for their sites? Anyone have any ideas what could have caused this? I know that none of our links are paid or otherwise junky.

Firstly, don't sweat it. Google only shows you a sampling of the sites it knows about. Just because your backlink count dropped doesn't mean that Google doesn't recognize your link on those sites anymore.

Just keep tabs on your traffic and make sure that this isn't a trend that is affecting your rankings and traffic from the SERPS.

If a decrease in backlinks goes hand-in-hand with a decrease in traffic, you might want to shoot a letter over to Google via Google Webmaster Tools asking if you're banned or blacklisted for any reason and if there's anything you can do to correct it. Prove that you don't buy/sell links and are upfront and honest with them.

Speaking of selling links - you wrote you don't buy any, but do you sell any? Do you do link swaps on your site that might be confused with something that looks like or might look like links that were paid for? If so, that could be what's hurting you.

Google might be thinking rest 2/3/ links you have bought and are not natural links.

Speaking of selling links - you wrote you don't buy any, but do you sell any? Do you do link swaps on your site that might be confused with something that looks like or might look like links that were paid for? If so, that could be what's hurting you.[/QUOTE]

We don't sell links or do link swaps, so neither of those could be an issue. I will do as you suggest and keep on eye on the SERPs and traffic (so far there doesn't seem to be any downward trends). Thanks for the reassurance!

On Google's next crawl my external links all "came back." Phew. Lesson learned: even with Webmaster Tools, the backlinks listed are just a (fuzzy) snapshot.

Thanks for the update. Glad it worked out for you.

Since they change their algorithms constantly, sometimes links won't show or count, I assume. For instance, I read they like links from PR4 or higher. Also, if you posted on forums, blog comments, etc. Those pages might have been archived or taken off by the owners, thus reducing your linkage. But, wouldn't worry, just keep building your links, it is a lifelong task for SEO folks..lol.