Editor rejected manuscript claiming it is similar to a not-yet-published manuscript (that I haven't seen). How to proceed? A few months ago, I submitted a manuscript. After the reviews were completed I received a rejection decision from the Associate Editor (AE). The rejection was based on the basis of a single rejection recommendation by one of the four reviewers. The journal has very high standards so this is not uncommon. However, the reason for the rejection appears really awkward to me. The reviewer wrote in his/her report that another paper with a similar idea was submitted (not published) in another journal. He/she wrote that the submission date of the other paper was earlier than mine so the originality of my idea is questionable. The AE agreed with this report and adopted this argument in the rejection letter.  

I want to emphasize that my results were independently developed and I have no knowledge whatsoever of the other manuscript which according to the reports that were attached has not been published yet. The whole situation seems rather awkward and I am not sure how to react. Of course the reviewer's identity is not known to me, but I find it hard to believe that he/she is not an author or somehow related to the author of the other paper. 

Furthermore, I feel really offended by these comments  as it appears to me that I am implicitly being accused of plagiarism. I am considering writing a letter to the Editor in Chief. I do not want to change the decision, but I would like to make clear that my results were independently obtained. Also, what are your thoughts on how should I proceed with my manuscript?
I don't think there is any point in writing to the EiC, if you don't want to actually appeal the decision.  I would simply send a note to the AE who handled the paper:


  Thank you for handling my paper.  I accept your decision.  I would simply like to state that the results in my paper were obtained independently, and I had no previous knowledge of the unpublished manuscript mentioned by Reviewer #4.  I will look forward to reading and citing this paper when it becomes publicly available.


Then submit your paper somewhere else, quickly (though after making any revisions suggested by these reviewers).  I would be inclined to include a comment to the new journal's editor, saying that you have heard there is a paper under review somewhere with similar results, but you have been unable to obtain a copy of the paper or any further information about it.  You could also emphasize that you have obtained your results independently of any other reseacher / group.