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This study reports the findings of a high-resolution melting (HRM) curve analysis combined with PCR technique (PCR-HRM) to differentiate between Muscovy duck parvovirus (MDPV) and goose parvovirus (GPV). A degenerate primer set was designed based on the VP3 gene of MDPV and GPV. The PCR HRM assay was able to discriminate between MDPVs and GPVs by differences in melting curve shapes and melting temperatures. A total of forty-five clinical samples, passaged in the allantoic cavity of Muscovy duck eggs, were detected by the PCR-HRM assay. Among the 12 positive samples, two were identified as MDPV and two as GPV with high genotype confidence percentage (GCP) values. Seven positive samples had low GCP values for the melting curve analysis and were identified as co-infection samples. One of the 12 positive samples, designed GDNX strain, was identified as a variant strain with a divergent melting curve profile. To assess the capability of PCR-HRM assay to distinguish MDPV and GPV, fifty-two field samples were collected and examined. Seven samples were positive for MDPV and/or GPV. Thus, this developed assay was useful for discrimination of MDPVs and GPVs and can also be suitable for detecting co-infection samples.