Q: How do I write a cover letter to a partner journal that I was referred to by the original journal?

Unfortunate that your manuscript was rejected by the original journal, but great that they referred you to a partner journal. This happens quite often.

So, writing the cover letter should be quite easy, as the earlier journal has referred you to this one. As you would have probably written a cover letter to the earlier journal too, you could keep this one similar to that, except for two things.

Firstly, you could let them know that you have been referred by the previous journal. Secondly, as you now know that there’s probably a better scope match with this journal, your cover letter should talk about just that: how your research fits with the specific focus of this journal. In fact, before sending your manuscript to the second journal, you should spend some time going through the journal site and also its articles (if they are open access) to get a better understanding of the type of articles this journal publishes. That way, you would be better explain to them how your paper does indeed fit with the focus of this journal, thus improving the chances of acceptance.

And for the cover letter content, you may find these resources helpful:

• 10 Tips to write an effective cover letter for journal submission
• Should I mention my submission history in the cover letter to resubmit my paper as new submission?
• A practical handbook of templates for communicating with the journal [Handbook]

Hope that helps. And all the best this time around!