There are less number of opportunities in India for zoology than anatomy as zoology includes animal behaviorist, animal trainer, etc where anatomy includes study of animal organs and you are allowed to work in hospitals or any other government medicine department to train the scientists dentists, doctors, etc. Also, salary of antomist varies from 2-10 lakhs per annum.
M.Sc. in Zoology and Anatomy are both 2 year postgraduate courses offered by many institutions in India. M.Sc in Zoology aims on developing advanced skills of animal structure, biology, etc, whereas M.Sc. in Anatomy focuses on advanced scientific study of human body.
You can go for either degree, depending on your eligibility and interest, as deep knowledge will facilitate you if you pursue Ph.D. in the subject too.
All the best