Can I resubmit a rejected manuscript to the same journal?

It depends. Most of the time, rejected manuscripts can be resubmitted to the same American Meteorological Society (AMS) journal if the concerns of the reviewers are addressed in a response to the reviewers in your cover letter. Usually, the decision letter will say something like this:

“Although your manuscript is being rejected, I invite you to once again carefully consider the reviews with a view to improving your manuscript and resubmitting it. Your work is of interest to our journal, and with appropriate revision could result in an acceptable and interesting paper. Should you decide to further revise your manuscript for resubmission, please submit both your new paper and your responses to reviewers to http://XXXXXX. (Your resubmitted manuscript will be given a new manuscript number.)”

In some cases of exceptionally poor-quality papers, we Editors may not encourage submission, and there may not be such a statement in the decision letter encouraging resubmission.

If it is ever unclear from the decision letter and you wish to revise your manuscript so substantially that it warrants another look by the same journal, I would suggest contacting the Editor and asking his or her opinion about whether you are welcome to resubmit it. Most Editors will give you an honest answer to such a question.

I admit that we AMS Editors probably don’t do as good a job as we should in conveying this information to authors of rejected manuscripts.

How Editors work at other journals published by other organizations may differ from the advice that I am giving you here. For instance, I know that if you get a paper rejected from some journals, they do not encourage resubmission. Some journals such as Nature Immunology do consider appeals.