If I do M.Sc from zoology and botany, which subject will I have to select for NET exam?

You need to opt for the same subjects in which you have done your PG.

If you have completed your M.Sc. Degree in both Zoology and Botany, you can choose the subject in which you want to appear for the National Eligibility Test (NET) based on your interests and career goals. The NET exam is conducted by the National Testing Agency NTA for determining the eligibility of

The same subjects that you studied for your degree must be your choice. Go for Zoology if you learned it; otherwise, choose botany.

Zoology is quite related to Environmental Sciences as all Zoology students must have to study Environmental Biology in their M.Sc. Not only Zoology candidates from other Life Sciences background. Hope it helps.