MD or PhD: who is the better choice for an LOR?

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won't make a difference imo. If you ask the MD she'll probably ask her husband for advice on what to write, but she won't be able to write as much as to your relationship with her. So you'll get the benefit of her name on the letter, but the content won't be as rich in comparison to a letter from the PhD.
 
If I were you, I would ask for a letter from a PhD (since he personally knows you better and will write a more in-depth letter) AND I would also ask him to have the MD cosign the letter. I think it will look really good and will be no problem for them.
 
Find yourself an MD/PhD.
 
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