I had an ultrasound and my right ovary has a cyst with a septation. what does this mean.

Depends: It could be anything from a functional cyst that will resolve to a tumor. In the tumor category, there are benign and malignant tumors. If there is a single thin septation, then it would most likely be a benign tumor. If there are thick septations or nodules, then more likely malignant. Size and your menopausal status are also important factors.

Usually nothing: Benign cysts can have little dividing walls or septations. If is of any other concern you can get a followup up ultrasound after a couple of cycles, should be gone by then.