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I was checking inbound links in Google Search Console and it says I have 1000s of links from some completely irrelevant domains.

They're not related to my industry whatsoever, they've all appeared in a short space of time, yet they don't have low trust metrics in either Moz or Majestic.

When I check the pages for links to my site, I can't find any. I'm not sure what to do - is Search Console reliable here? Should I submit these domains to the disavow file even though I can't actually find a link to my site?

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  • The websites could be cloaking and showing Googlebot a different version of the page with your link in it.
    – Stephen Ostermiller ♦
    Jan 31, 2018 at 14:40
  • This is a common spammer tactic. New cheap domain names or domains that recently expired are used to create sites that create spam sites quickly. These may only be spammy for a day or hours before reverting. Part of this is creating links that come and go very quickly. Not sure what the payoff is exactly, it is hardly efficient as a spam tactic, however, with spam small numbers count and over thousands of domains, those small numbers really add up. This tactic is also sometimes used on hacked sites.
    – closetnoc
    Jan 31, 2018 at 15:41

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It does not hurt your site if you add these links to the disavow file nonetheless. As @closetnoc said, it could've been part of a spam tactic, so these pages might not be available any longer for now - but I'd surely recommend to add them to the disavow file just to make sure they are not being evaluated by Google in your backlink profile - especially if these links might still persist, but just not be available to you (cloaking, as @Stephen Ostermiller mentioned). (Please keep in mind, though, that the disavow file is only available for Google; if you've got any relevant traffic by other search engines such as Bing, you need to handle these separately.)

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Make sure you have Search Console setup for the http://www.yourdomain.com also http://yourdomain.com, in addition to any other subdomains like https://www.yourdomain.com. You can also verify links with an additional backlink crawler. Remember you are looking at diverse indexes by diverse data sources, so you will see some disparity in results (diverse numbers and links for diverse backlink reports.)

To get an improved understanding around your backlink profile my commendation is to use a pair of tools (OSE, Majestic, aHrefs, etc) in addition to the data delivered in Search Console. Export the backlink information from all sources into Excel, de-dedupe the statistics (so you're not seeing at duplicate links) and review where the links are coming from. Using more than 1 tool will provide you a much better understanding what is out there, so see which ones work for you and your budget.

Also, ensure you have the precise version of your site in Search Console. Google will identify multiple disparities as diverse sites (HTTPS/WWW/HTTP/Non-WWW). You'll also want to set a favored domain (www vs. non-www) to aid Google in combining data.

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Google Webmaster Console should tell you the page URLs of the inbound links it has discovered that are pointing to your site. You can view them in the URL below where siteUrl=yoursite and blddomain=theirsite

https://www.google.com/webmasters/tools/external-links-domain-to-page?hl=en&authuser=0&siteUrl=example.com&bldomain=example.com

The list on that page should tell you the pages that are linking to your website that Google has discovered. When you visit those URLs you'll get a better sense if those domains are performing spammy behavior, if the links are legit, or if they simply once linked to you but have since updated their page and removed the link.

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