Tax forms are only one way of proving a bonafide marriage. If you have children together and evidence of shared finances, you should be OK. You might want to see an article I wrote on this subject. Best of luck.
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I agree with my colleague. It is important for you to have other evidence of your bona fide relationship, and it seems like you have that. You should also be prepared to explain why you are filing separately at your interview if the issue comes up.
My colleagues addressed the tax issue.
I have a greater concern. If you've been married for 3 years ... why haven't you filed for his green card yet?
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