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@HRP20 wrote:

Yes both homes in California. We still see each other, but live separate as healthier for our relationship.


If you are both permanent residents of California, you can file jointly if you prefer, and the state won't care that you live in separate homes.  The only issue might be that you will only have one address on your tax return, this is where you want tax-related mail to be sent.  It does not have to be the address where you live.  It can be either home, or a PO Box, or even a relative whom you trust.  

 

If you did want to file separately (married filing separately) then you would file MFS for both the federal and state, and you would each use your own address on your own return.