The answer is very simple: under the facts as you've described them, no, you wouldn't be allowed to file a joint return with your estranged wife. The basis for this depends on whether or not you and your wife have a decree of separate maintenance; that is, has a court decreed that the two of you are separated? If so, then you should be treated as "not married" under section 6013(d) of the Internal Revenue Code and therefore not eligible to file a joint return. Instead, you each must file as single.
Given that the space for posting facts here is limited, and there may be relevant facts you haven't thought about, I would strongly suggest that you speak to a competent local tax attorney who has experience with individual tax return matters. Please do not just rely on the answers you get for free here; remember, you usually get what you pay for.
Well that is because we are on an online message board and we cannot ask all the facts we need to make a fully informed answer. i suggest you talk to your divorce attorney who you have paid to do the legal separation. That is the person who is being paid to represent you and to answer all your questions. Then the conflict is within the IRS regulations and not the lawyers? I suggest you retain counsel that has expertise in IRS law. A message board is not suppose to be the end all to your legal issues. I understand your frustration but it sounds like we cannot help yo any longer here. It also begs the question are you talking about late filing for 2011 or about 2012? It also begs the question are you so sure filing with your spouse will be helpful. The key difference in the IRS regulations may be the use of the word "maintenance". I would then ask is your wife receiving maintenance? The IRS most likely has some issue with the benefit you will receive (or not receive as the case might be) for claiming the maintenance as a deduction while filing jointly with the person receiving the maintenance. This is just a hunch but I do think I am on to something here. As you seeing I am trying to help. I have already answered this question when previously posted. All lawyers who are poster use our own free time to answer questions on this forum as a pro bono activity.
IF YOU FOUND THIS ANSWER HELPFUL PLEASE MARK IT SO. This information is provided by PEGGY M. RADDATZ, Attorney At Law as a pro bono service. YOU SHOULD CONSULT WITH AN ATTORNEY IN PERSON who has specific expertise in the area of law you are asking about.
You are on the right track. You must look at the last day (Dec. 31st) of the tax year and ask yourself are you still married on that day. If on that day you are divorced or legally separated BY DECREE or JUDGMENT, you cannot file jointly.
As an FYI, you will need two married people to file jointly AND both have to consent to it as both parties will need to sign off on the return. So, even if you were married at the particular time and your ex-spouse does not want to file jointly (no matter how irrational that may be), he or she is not obligated to do so. Thus, you would be limited to either married filing separate or head of household (if applicable).