Single cell PCR analysis and light and scanning electron microscopic techniques were utilized to identify free living bivalve larvae in the coastal waters of Tae-an, on the west coast of Korea. Through DNA sequencing, venerid clam larvae were isolated and identified as Ruditapes philippinarum (99% similarity) and Meretrix lusoria (99%). Under microscopic observation, the D-veliger stage of R. philippinarum exhibited symmetrical shoulder angles and an elliptical ventral form. In contrast, M. lusoria displayed asymmetrical shoulder angles and a round ventral form in the umbonal stage. Size of the R. philippinarum larvae was $156{pm}22{mu}m$ in length, $126{pm}12{mu}m$ in height, $92{pm}14{mu}m$ in width with a length: height ratio of 1.23. Meretrix lusoria was $202{pm}44{mu}m$ in length, $161{pm}35{mu}m$ in height, $96{pm}38{mu}m$ in width with a length: height ratio of 1.25. Experimental results indicate that morphological and molecular characteristics provide evidence for the larval identification of these two venerid clam larvae species in nature.