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So all tools (including Search Console) have different link indexes they're going to show you. That's one reason why you're seeing a difference between tools. The other reason is that Search Console will only show a **sample of your links, not all of them. **To really find all internal links, you should use a crawling tool like Screaming Frog or Xenu then check inlinks and outlinks on your site. I wouldn't rely on Search Console to give as much insight on your internal linking. To get a better understanding about your backlink profile my recommendation is to use a couple of tools (OSE, aHrefs, Majestic, etc) in addition to the data provided in Search Console. Export the backlink data from all sources into Excel, de-dedupe the data (so you're not looking at duplicate links), and that will help you understand your profile a little better. Using multiple tools will be a little on the expensive side, but will give you a much better understanding what's out there. Like Justin said, make sure you have the correct version of your site verified in Search Console. Google will recognize multiple variations as different sites (HTTP/HTTPS/WWW/Non-WWW). You'll also want to set a preferred domain (www vs non-www) to help Google consolidate data.