Right now, Facebook comments work just as well for SEO purposes, as Wordpress native commenting.
The advantage of using Wordpress native commenting is that it's already set to go and you don't have to do anything special to put it on your blog. Just select your settings, and you're off and running. Of course, it's a good idea if you go this route to install and utilize something like Akismet, to automatically detect and root out spam. Nothing worse than spammy comments.
The advantages of using Facebook comment plugins are:
- Most people have Facebook and are already logged into it, almost all the time.
- The viral sharing function of Facebook
- You get access to knowing a lot of information about the people commenting and interacting with your blog.
However, if you think people may want to comment in privacy, then Facebook is not a good idea. While they can certainly select settings to protect their privacy, most people won't go that extra mile. They'll be turned off by the extra effort, and just not comment at all. This all comes down to the type of blog you're running, and your demographic.
Also, remember that at any time Google could choose to stop indexing Facebook comments, or Facebook could make their comments un-indexable by Google... These are pretty big risks.
Neil's overall advice: go with Wordpress native commenting, and get a couple of powerful plugins to make it run like a well-oiled machine.
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