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I have 2 sites with very similar HTML structure and I would like to know how google or any other crawler rank these 2 sites.
Will they penalize me due the sites sharing a structure?
The content itself is unique to each site, but the underlying HTML structure is basically the same, with each site having a unique brand stylesheet.
Does this make an impact on how the sites will rank?
You should read the duplicate content post on Google guidelines.
Duplicate content generally refers to substantive blocks of content within or across domains that either completely match other content or are appreciably similar. Mostly, this is not deceptive in origin.
It doesn't matter if your browsing directory or even template is the same in both domains as long as the content in each one is unique and generates value to users and searchers.
