We investigated the spawning areas of the two lineages of sand lance, A. personatus, in Korean waters to indirectly elucidate their gene flow. A larval survey was conducted at 59 stations in the Yellow Sea (YS, 2006–2008, 2013), 42 stations in the Korean Strait (KS, 2009–2011), and 30 stations in the East Sea (ES, 2012–2014) using ichthyoplankton nets. In total, 8687 inds./100 m3 were collected in the YS and ES and identified as sand lance larvae. In contrast, no sand lance larvae were found in the KS. The number of sand lance larvae was highest in the middle ES, followed by in the middle YS. We identified the lineage status of 227 larval individuals using molecular methods. Only a single lineage (south lineage; SOL) occurred in the YS, whereas two lineages (SOL and the north lineage, NOL) occurred in the ES. The larval occurrence of NOL was much higher than that of SOL (5.2:1) in the middle ES, but the two lineages occurred at similar levels (1.1:1) in the southern ES. These results suggest that there is no gene flow between the two lineages in the YS, whereas there is restricted gene flow in the ES.