Systems and methods for mapping affiliated graphs using video fingerprints are disclosed. Some embodiments include receiving first media corresponding to a first package encoding of a video content; identifying a first set of frames of the first media and generating video fingerprints for the first media; receiving second media corresponding to a second package encoding of the same video content; identifying a second set of frames of the second media and generating video fingerprints for the second media; generating a mapping comprising alignment information of one or more frames of the first set of frames and one or more frames of the second set of frames; and outputting the generated mapping for determining a switch point for switching from the first package encoding to the second package encoding during display of the video content.