I installed Anaconda 5.3 with Python 3.7 (root environment).
After that I created a new environment (py36) using Python 3.6

I activated the new environment with activate py36
conda env list shows that the environement is active.

But when I start Jupyter Notebook (from the Anaconda prompt with jupyter notebook), it seems to use the root environemt, not the activated environment.

How can I use Jupyter Notebook with the new create environment (py36)?

As @Ista mentioned, the documentation gives an easy solution using notebook extensions.

conda install nb_conda

After installing, you have the option in Jupyter Notebook to 'Change kernel' from the 'Kernel' menu in your Jupyter Notebook.