Three specimens of Cynoglossidae larvae were collected from the southern Korean Sea in May and August of 2009, and were identified using morphological and molecular analysis. Specimens were divided into two groups based on the number of elongated dorsal fin rays on the top of the head: Cynoglossidae sp. A was defined as having two elongated dorsal fin rays, while Cynoglossidae sp. B possessed a single elongated dorsal fin ray. One specimen of Cynoglossidae sp. A, a post-larva with a notochord length (NL) of 5.8 mm was thought to be a Cynoglossus joyneri larva based on the presence of 115 dorsal pterogiophores, 85 anal pterogiophores, and 50 myomeres. Two specimens of Cynoglossidae sp. B, a 4.1 mm NL larva and a 11.3 mm NL juvenile, were thought to be Cynoglossus abbreviatus based on the presence of yolk in the former and 133 dorsal fin rays, 105 anal fin rays, and 63 myomeres in the latter. To test this morphology-based identification, molecular analysis was conducted using 419-422 bp of mitochondrial DNA 16S rRNA. Cynoglossidae sp. A was clearly matched to a Cynoglossus joyneri adult (d=0.000) and Cynoglossidae sp. B clustered closely with Cynoglossus abbreviatus adults (d=0.002). A neighbor-joining tree supported this robust relationship (bootstrap value=100%). Therefore, these molecular data validate the morphological identification of the two Cynoglossidae larval species.