I did my B.Sc botany with 55% aggregate in 2016. Am I eligible for M.Sc zoology?

Yes, you are eligible to pursue M.Sc. In zoology. If you are concerned about the gap in between then don't worry. You will only be required to give a Self Declaration stating your reason for the gap and then you will be allowed to take admission.

You are eligible for M.Sc in zoology if you had zoology as a subject in your graduation but with this percentage it might become difficult for taking admission in universities but you may apply in some private colleges offering M.Sc. In zoology. I hope this might help you.