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Deductions & credits
Taxpayers using the Married Filing Separately status do not qualify for the dependent care credit.
In addition, funds put into an FSA for dependent care are already "pre-tax". This means you've already gotten a tax benefit for these amounts. Therefore, no additional credit would be allowed for the same amount. If you have expenses in excess of the FSA and use a different filing status, then you may still qualify for a dependent care credit.
In regards to putting money into both of your FSA's, the rules say taxpayers that are filing separately can put up to $2,500 into their FSA. This means that each of you can put the maximum of $2,500 into your Dependent Care FSA; however, you can only use your dependent care expenses one time when requesting reimbursement.
When you
prepare your tax returns, the spouse that does not intend to claim the
child should still enter them as a dependent and indicate that the other
parent will claim the child. This allows the child to show up in the
Dependent Care Credit section for determining if you had any excess FSA
benefits that may be taxable.