I have a main portal with different sub sites. I want to add link to different css file for each subsite. One way of doing it would be creating different masterpages for each subsite, which doesnt look like a good option. Is there any other way of linking different css depending on the visiting site

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You can use the AlternateCSS property on each site. Which can be set by code or manually but you need to have the publishing feature turned on in order to make it work.

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