Plaice (Pleuronectes platessa) and flounder (Platichthys flesus) are economically valuable flatfishes found on the European shelf that are known to naturally and artificially hybridize. Putative hybrids have intermediate coloration which suggest an interspecies status between plaice and flounder. To further investigate this hybridization process, genetic testing was performed on individuals from morphologically identified hybrid samples from the Baltic Sea. Morphological examinations indicate that putative hybrids are morphologically more similar to plaice than flounder. Putative hybrids are difficult to differentiate from plaice without thorough morphological examination. However, the number of vertebrae and scale thrones can morphologically differentiate plaice, flounder, and putative hybrids. Purebred plaice and flounder samples were well-discriminated by nuclear markers TMO-4c4, pthrP, and microsatellites. The analysis results showed that the genetic status of some putative hybrids were in an intermediate position between their parent species populations, which confirmed their hybrid identities. Mitochondrial marker COI results suggest uni-directional maternal material contributions from plaice for this hybridization process. Despite consistent sampling effort at all study sites, putative hybrids were only observed along the western edge of the Baltic Sea and not found in the further west or northern sampling locations.