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That really depends on why the one site is ranking higher.  Is it's content better?  Google doesn't really care about how nice the site looks, but real  people do. If you are just now launching a website for your company/organization, it is probably advisable to have only one or you will be competing against yourself - your competitors will reap the rewards.  Keep the domain that is performing better. Do some searching about 301 redirects when you move to one site.