Did you get a marriage certificate from the County Clerk's office? If yes, then the religious ceremony is proper. You can got custody and or visitation even if you are not married providing you are the biological father of the child. You would need to file with the family court where the child is located. Consult with a local family law attorney to help yoy.
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Religious ceremony without an official certificate of marriage does not make the marriage legal.
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Dear New York Spouse:
Marriages in New York State require a marriage license prior to the solemnization of the marriage in a religious ceremony.
New York City has its own special rules relating to the marriage license:
The answer provided to you is in the nature of general information. The general proposition being that you should try to avoid a bad outcome if you can.