In terms of the broader evolutionary relationships between the giant freshwater whipray and the rest of the family Dasyatidae, a 2012 phylogenetic analysis based on mitochondrial DNA reported that it was most closely related to the porcupine ray (Urogymnus asperrimus), and that they in turn formed a clade with the mangrove whipray (H. granulata) and the tubemouth whipray (H. lobistoma).
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