Simple SummaryThe European flounder (Platichthys flesus), which is closely related to the recently discovered Baltic flounder (Platichthys solemdali), is currently the third most commercially fished species in the Baltic Sea. The aim of this study was to obtain information on the current patterns of genetic diversity and the population structure of the European flounder and to verify whether the Baltic flounder is present in the southern Baltic Sea. Moreover, we aimed to verify whether the observed decline in the body condition indices of the species in the Baltic Sea might be associated with adaptive changes in its gene pool due to increased fishing pressure. The examined European flounder specimens displayed a high level of genetic diversity and represented a single genetic cluster. The applied molecular markers did not detect the presence of the Baltic flounder among the fish sampled from the studied area. Correlation analysis between genetic and morphological characteristics did not detect any signs of directional selection or density-dependent adaptive changes in the gene pool of the examined fish.AbstractThe European flounder (Platichthys flesus), which is closely related to the recently discovered Baltic flounder (Platichthys solemdali), is currently the third most commercially fished species in the Baltic Sea. According to the available data from the Polish Fisheries Monitoring Center and fishermen’s observations, the body condition indices of the species in the Baltic Sea have declined in recent years. The aim of the present study was to obtain information on the current patterns of genetic variability and the population structure of the European flounder and to verify whether the Baltic flounder is present in the southern Baltic Sea. Moreover, we aimed to verify whether the observed decline in the body condition indices of the species in the Baltic Sea might be associated with adaptive alterations in its gene pool due to increased fishing pressure. For this purpose, 190 fish were collected from four locations along the central coastline of Poland, i.e., Mechelinki, Władysławowo, the Vistula Lagoon in 2018, and the Słupsk Bank in 2020. The fish were morphologically analyzed and then genetically screened by the application of nineteen microsatellite DNA and two diagnostic SNP markers. The examined European flounder specimens displayed a high level of genetic diversity (PIC= 0.832–0.903,I= 2.579–2.768). A lack of significant genetic differentiation (Fst= 0.004,p> 0.05) was observed in all the examined fish, indicating that the European flounder in the sampled area constitutes a single genetic cluster. A significant deficiency in heterozygotes (Fis= 0.093,p< 0.05) and overall deviations from Hardy–Weinberg expectations (H-WE) were only detected in fish sampled from the Słupsk Bank. The estimated effective population size (Ne) among the sampled fish groups varied from 712 (Słupsk Bank) to 10,115 (Władysławowo and Mechelinki). However, the recorded values of the Garza–Williamson indicator (M= 0.574–0.600) and the lack of significant (p> 0.05) differences inHeq>Heunder theSMMmodel did not support the species’ population size changes in the past. The applied SNP markers did not detect the presence of the Baltic flounder among the fish sampled from the studied area. The analysis of an association between biological traits and patterns of genetic diversity did not detect any signs of directional selection or density-dependent adaptive changes in the gene pool of the examined fish that might be caused by increased fishing pressure.