I am a B.Sc last year student and my subject is zoology and botany. In which subject should I pursue M.Sc?

If you are unsure, then go with Botany. It is easier of the two and has same scope as zoology. Try to consult your teachers too. They know you better and would tell you accordingly.

It totally depends on your interest if you are interested in zoology, then opt for zoology in your Masters. Otherwise, go with botany and both subjects has a equal opportunity of jobs.