Well, just that one thing is not going to cause a denial of your case. The more you have of the following, the less of an impact that filing married but separate will have:
A letter where you describe, in a very detailed fashion, the circumstances in which you met your spouse, the reasons you married, and the feelings and emotions that you have towards your spouse, and why.
If you have a child or children together, the birth certificate for each child.
Wedding pictures and pictures of other moments when you and your spouse, and other members of your families and friends have been together.
Very detailed letters from people who know you and your spouse and who are witnesses that your marriage was valid, who were at your wedding, or who knew you as a married couple.
Love letters or cards that you received from your spouse while in the relationship.
Letters from people addressed to both you and your spouse, or in which the person who wrote the letter refers to both of you as a couple.
Any types of documents that have both your names on them that show that you bought a car, a house, furniture, or anything else together.
Any rental or lease agreements for your home or apartment with both of your names on it or a letter from the building manager or owner proving that you lived together.
Bank or financial statements that show that you had or have a savings or checking account together.
Any insurance documents that show that you were or still are covered by your spouse's insurance plan, or that your plan covers or covered him or her.
Bills, such as electricity, water, heat, cable TV, phone, or others that show both you and your spouse's names.
Jointly-filed Income tax papers (both your names).
An identification card that shows that you use your spouse's last name.
Membership cards for video clubs, grocery stores or similar businesses, that show joint membership.
Any other documents that prove your relationship.
So the more you have, the better it is. In the end, you will both have a chance to explain that to the interviewing officer. As long as it is a reasonable reason that doesn't show that maybe the marriage is not real, the officer should have no problem with it. I had a couple as clients once that they did not have bank accounts together and the husband explained that his wife spent money like water and couldn't control herself so he didn't want her touching his money. It was a valid reason and they were approved because they had so many other things together.
So just collect as much evidence as you can and you should be ok. Please let me know if you have additional questions and please do not forget to rate my service to you (not the state of the law) as that is the only way that I can get credit for my assistance.
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