Nucleotide sequence analysis of 18S ribosomal RNA gene (rRNA), internal transcribed spacer, and 5.8S rRNA was used for taxonomic identification of ctenophores collected in the northern Baltic Sea, where invasive Mnemiopsis leidyi and native Pleurobrachia pileus have been reported to occur. Contrary to previous reports, sequence analysis of 53 randomly selected specimens from seven stations revealed that none of them were M. leidyi or P. pileus. The 18S rRNA and 5.8S rRNA sequences were 100% identical to those of Mertensia ovum, a ctenophore with a broad Arctic and circumboreal distribution, which has never been reported to occur in the Baltic Sea. Polymerase chain reaction screening with primers designed to amplify all three species, and using ctenophores collected by vertically stratified sampling, confirmed that all ctenophores collected in this survey were M. ovum. The ctenophore abundance was high, up to 4500 individuals m 22 , positively correlating with salinity. Our findings emphasize the utility of applying molecular tools to biological surveys and the importance of rigorous species identification. They also indicate that M. leidyi, which is a threat to the southern Baltic ecosystem, does not occur in the northern part of the sea, and call for a pan-Baltic survey to establish current distributions of ctenophores, both native and invasive.