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QGIS uses it's own Python path, which gets set when you launch QGIS (this should be done automatically). But if you are having issues with Python in QGIS try launching it from the QGIS.bat file from \OSGeo4W\bin or \QGIS install path\bin, depending on the installation location. ArcGIS takes over the system one. So you are fine to have both installed.

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