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I am working with a site which we'll call www.newdomain.com, which was hit by Penguin this month despite no unusual practices.

I found lots of really spammy links to their old site, www.olddomain.com, which 301s to the new domain.

So I've gone through the process of identifying which links are really bad, made contact to ask for removal, and am at the stage of disavowing links.

But wait!

None of the bad links point to newdomain.com, and I worry that a disavow request via this domain in Webmaster Tools will damage something.

  1. Do the old band links affect the new site?
  2. If so, where do I disavow those old bad links? On Webmaster Tools for the new domain?
  • Did you receive a email stating that your site had been hit? reason I ask is that many people confuse penguin with every day algorithms. Google's algorithms can drop a site just as badly as Pengiun, Also another factor is that Google recently unpunished a lot of Pengiun-hit sites so huge shifts lately have been of people getting their rankings back which of course doesn't mean you gone down in rank but rather they have gone up. You should only ever use the disavow tool if your sure that you've been hit which is normally a message received in Webmaster Tools. – Simon Hayter Nov 6 '13 at 17:58
  • Also to add, if the old site was hit by Penguin then using a redirect 301 from old to new will pass that Penguin across, this takes time to take place, otherwise Penguin would be pointless. – Simon Hayter Nov 6 '13 at 18:02
  • The hit was within a day of the new Penguin update. – RoosterTom Nov 7 '13 at 9:42
  • Then most likely the new site is Penguinalized because it's 301 redirected. If Google ignored it then every one would be doing it and Penguin would be pointless. And from personal experience the disavow tool rarely works or it takes absolutely ages to kick in, like 3months. Many people recommend ditching sites such as what your referring to, because its actually faster to rank a new than get a site out of a penguin, so a lot of people build new sites and leave the old site along and hope it returns that why if it does you have 2 sites ranking rather than one, and one that is extremely clean. – Simon Hayter Nov 7 '13 at 16:02
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None of the bad links point to newdomain.com, and I worry that a disavow
request via this domain in Webmaster Tools will damage something.

Do the old band links affect the new site?
If so, where do I disavow those old bad links?
On Webmaster Tools for the new domain?

Yes, old bad links affect the new site via redirects. Disavowing on the new domain won't help.

However, disavowing on the old domain may help. If you decide to go for it, you must be very aggressive and patient. I mean disavow anything suspicious. If a page is suspicious, then disavow the whole corresponding website. This likely means you will not recover the rankings you had before, because you didn't deserve these in the first place.

Another strategy is to move the valuable content from the old site to the new site and to remove all redirects. It would take some time to rank again, and probably not as high as before, but it would be better than nothing.

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If your old domain has bad links and passing negative value to the new domain you should not use 301 redirects. The main purpose of the 301 redirection is to pass all link juice of old domain to the new domain. If your website has bad links and you want to live a new domain why do you want to redirect the old to new? You have a benefit to start working in a good manner and create good links for your new domain. You can also follow JVerstry point that "Another strategy is to move the valuable content from the old site to the new site and to remove all redirects".

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