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Records about morphological abnormalities in rays of the genus Myliobatis are scarce worldwide. In the present study, three specimens exhibiting different malformations were identified during the monitoring of the reproductive biology of the Chilean eagle ray Myliobatis chilensis, conducted from 2017 to 2018 in the fishing port of Salaverry (northern Peru). The identified specimens included: (i) a female with split pectoral fins, (ii) a male with an unfused-to-the-head pectoral fin, and (iii) a female with a short and thick tail. Here we report and discuss the implications and likely causes of these first three cases of morphological abnormalities in M. chilensis from the western Pacific.