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I graduated from my undergraduate institute back in 2012 and just got out of the Navy after 5 years. I'm applying this fall, but my current plan is to have two professors from my undergraduate days write me letters. They both knew me well and I think they can write very good letters, but I'm worried it might be suspicious that I'm not getting anyone from my 5 years in the Navy. Also, I have taken some graduate level courses since 2012, but I'm not getting LoR from anyone who taught those classes, even though they will show up on my transcripts, since they were all online courses and I never got to know any of the professors well. Will this be suspicious too?

You're taking the right approach. Schools prefer letters from professors who actually know you, and no, no one will think this is suspicious.