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If you filed joint federal tax return - and one spouse is non-resident of CA with no CA-source income - you may file CA tax return either as MFJ or MFS.
If you file CA tax return as MFJ - you will use the form 540NR - http://www.ftb.ca.gov/forms/2008/08_540nrca.pdf to determine CA taxable income.
A nonresident is only taxed on income derived from California sources.
see instructions here - http://www.ftb.ca.gov/forms/2008/08_540nrcains.pdf
In Hawaii - if you file a joint tax return - all income from both spouses will be taxable.
You may prefer to file Hawaii tax return using MFS status.
See check box on the line 3 - http://hawaii.gov/tax/2008/n11_i.pdf
In additional - see instructions for the form N-11 - http://hawaii.gov/tax/2008/n11ins.pdf
A nonresident married to a Hawaii resident may choose to file a joint return with the resident spouse on Form N-11 or N-13; however, the nonresident will then be taxed on all income from all sources.