From http://reliablybroken.com/b/2012/05/custom-template-folders-with-flask/

flask.py

import flask
import jinja2

app = flask.Flask(__name__)
my_loader = jinja2.ChoiceLoader([
    app.jinja_loader,
    jinja2.FileSystemLoader('/path/to/extra/templates'),
])
app.jinja_loader = my_loader

@app.route('/')
def home():
    return flask.render_template('home.html')

if __name__ == "__main__":
    app.run()