In this study, we analyze a genomic dataset of ultraconserved-element and mitochondrial loci to construct a phylogeny of the Polynemidae. Our molecular dataset included 450 ultraconserved element loci and one mitochondrial locus. Our analyses of these data recovered threadfins as a clade sister to flatfishes, with the most taxonomically rich genus, Polydactylus, being resolved as polyphyletic. When comparing our dataset to data from previous studies, we find that a few recent broad-scale phylogenies of fishes have incorporated mislabeled, misidentified, or chimeric terminals into their analyses, impacting the relationships of threadfins they recover. We highlight these problematic sequences, providing revised identifications based on the data sequenced in this study. We then discuss the intrarelationships of threadfins, highlighting morphological or ecological characters that support the clades we recover.