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Phylogenies based on morphological and molecular data confirm the monophyly of the subfamily Stelliferinae; however, there is no consensus on the intergeneric and interspecific relationships in the group. Previous studies suggested the non-monophyly of Ophioscion and Stellifer , and possible cryptic species in Ophioscion punctatissimus . Therefore, we used mitochondrial (16S rDNA and COI) and nuclear (Rhodopsin, EGR1, and RAG1) regions to examine phylogenetic relationships among species of this subfamily. Our results confirmed the monophyly of Stelliferinae and supports the close relationship among Bardiella, Corvula and Odontoscion , which form a sister group to Stellifer and Ophioscion. Notwithstanding, all the results support the non-monophyly of Stellifer and Ophioscion and we suggest that a taxonomic revision should consider Ophioscion as a junior synonym of Stellifer . Moreover, O. punctatissimus was grouped into two clades, with the O. punctatissimus lineage I (LI) being closer to O. scierus from the eastern Pacific than to the O. punctatissimus lineage II (LII). The most recent common ancestor (TMRCA) for the O. scierus and O. punctatissimus LI and O. punctatissimus LII clade dates from 7.2 (HPD: 4.3–10.5) Ma, whereas TMRCA for the O. scierus and O. punctatissimus LI clade dates from 5.3 (HPD: 2.4–8.6) Ma, indicating that speciation processes may be related to the rise of the Isthmus of Panama. Phylogeographic analyses corroborate the hypothesis of speciation in O. punctatissimus . These results suggest that lineages of O. punctatissimus originated from distinct ancestors and, by morphological similarity, were considered the same taxon. A taxonomic revision should be performed to validate the species status of such lineages. [ABSTRACT FROM AUTHOR]