In most cases, adult fish can be easily identified based on the analysis of morphological characteristics. In contrast to this, a successful identification of processed specimens or early life cycle stages might be quite challenging. Here we present an in situ hybridization (ISH) approach for reliable species identification. Oligonucleotide probes targeting the small ribosomal subunit (18S rRNA) were developed and tested for the identification of the three commercially important fish species Merluccius merluccius, Scomber scombrus, and Trachurus trachurus. These species are routinely monitored by triennial ichthyoplankton surveys in the Northeast Atlantic. Our results demonstrated a species specific hybridization and staining for all three target species using a combination of helper, competitor and probes. The Trachurus trachurus probe can also be used to identify Trachurus mediterraneus which can be found further South. Additionally, we showed successful hybridization by a subsequent use of probes. The application of in situ hybridization may represent a robust, fast and cheap alternative for the identification of fish species in comparison to other molecular approaches.