I'm guessing there's a virtualenv discrepancy between where you're running Flask and where you think you're running Flask. Multiple virtualenvs in conjunction with a system Python install can be tricksy to manage, but this will definitely be a local issue on your machine, so there will be a limited amount of help we can give in a general forum.
One of the things you can do to help diagnose what's going on is to drop import sys; print(sys.executable) into your script. This will show you which python is being used to run that script. From there, you can see the packages available to that environment by running path/to/python -m pip freeze from the command line.
Hope this helps.
