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This study aimed to enhance our understanding in monogenoid evolution by using morphological and molecular data to determine kinship relationships between species and changes in morphological structures over time. We focused on variations in characteristics among the organisms of the family Gyrodactylidae, concentrating on the phylogenetic position of Polyclithrum with other genera in the family. We collected specimens of Polyclithrum from the striped mullet, Mugil cephalus and Swingleus, and Fundulotrema specimens from mummichog Fundulus heteroclitus in estuarine systems of South Carolina, United States. In addition, we analyzed them and other genera (including e.g., Mormyrogyrodactylus, Gyrodactyloides, and Macrogyrodactylus) using both morphological and molecular (18S rDNA) approaches. We performed phylogenetic trees based on Maximum Parsymony, Maximum Likelihood and Bayesian Inference, and constructed a character morphological matrix by Parsimony Reconstruction of Ancestral Character States method. Our results suggest a homoplastic origin with evolutionary convergences in characters, revealing that there is inconsistency between our data and previously published works based solely on morphological structures of the group. The homoplasy scenario found in Gyrodactylidae can be a result of the limited set of putative homologous morphological features. However, differences between the phylogenies based on morphology and those based on molecular data may arise from both databases. While morphology remains essential in understanding the evolution of this group, molecular data, otherwise, provide a less biased source of information for constructing phylogenetic hypotheses. Combining these data facilitates a better comprehension of the homologous status of morphological features and to understand Gyrodactylidae evolutionary history., (© 2023. The Author(s), under exclusive licence to Springer Nature B.V.)