Also, should you include your reason or is it somewhat of a "right" and none of the editor's business? I've read that editors tend to get annoyed when writers want to use a pseudonym to "hide" themselves, but frankly I tend to get paranoid about people googling my name and finding my article online. Plus, at this point I'm not confident enough of my writing skills to want anyone I know to know how I write.
On the manuscript, your by line should be your pen name, but the contact information should contain your real name. In your query letter and all communications with the prospective editor, you use your actual name and contact information. This is the case regardless of whether you are seeking to publish a short story or a novel. I don't know how most nonfiction editors feel about pen names. It may depend on the subject matter.
To add to what Cogito indicated, sometimes with a submission (especially those uploaded via an online form) there is a spot for a pen name. I've never come across editors getting annoyed with pen names, but I'm sure it happens on occasion. If so, maybe that's not the right market for you. Terry
Don't forget on your letter (and elsewhere where you need to use your real name) to put "a/k/a [your] penname" after your real name (so the editor or editor's staff will know the manuscript by "penname" is actually yours). Assuming you keep a copy of that letter, it also helps you remember what you've submitted to whom and under what name (which I've seen cause problems for a writer or two who might've used one too many variations). The use of a penname doesn't really require any explanation at all. There are tons of reasons to use pennames. The issue of "hiding" behind a penname being something to be ashamed of, in my experience, comes primarily from other writers who seem to think there's some inherent virtue in the honesty of disclosing who you are to your readers. I don't know any reason to worry about any of that, myself. I hope I'm more than my name, after all (certainly so as a writer). Unless you're a celebrity (and they usually come with a pseudonym already built in), it's the work itself that usually matters, even to your immediate family. And they can sometimes be the first to understand why the penname is useful. Plus, pennames are fun and sometimes a "freeing" device. So, go for it.
Again, I think that it depends on the situation. If you feel too uncomfortable using your real name, just say so. They want the conent after all. If the pen-name is something like "Alyssa Jones" and not "Writewizard", I don't see why they'd have a problem with it. -ww-
Really, you don't even have to say using your real name makes you uncomforatble. Most publishers who are professional won't care either way a work is attributed (real name or pen name). If your real name was recognizeable, like you'd published a number of horror novels or stories for example, they may prefer you to publish under your real name...but that is a decision the writer gets to make, even if it means they won't accept the piece under the pen name. And here I am just trying to present a reason where it would make a difference. Just remember, any reputation you build up under your pen name (if any) won't likely carry over to your real name or other pen names. Terry
However, if you become well known under one name, publishers will want the tie-in to the famous name. For example, books written under the name Richard Bachman are appearing on shelves again now, as [by] "Stephen King, writing under the name Richard Bachman."