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No need to use rem’s for media queries – the value em’s obtain is that of the user agent, and not from your styles:

I’ve used em’s with the assumption that 1em ~= 16px in media queries for a while now. I discovered this after being baffled as to why my breakdpoints weren’t working, and eventually discovering that no matter what I had set my base font size to, media queries were consistently being calculated at +-16x the value of the em in the media query.

Don’t worry about fallbacks – just use em’s for media queries, and use rems as you’d want everywhere else.