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The Norwegian Food Safety Authority recently stated that stomach flushing is in violation of the Animal Welfare Act. The objective of our research was to develop a genetic method for the routine identification of Lepeophtheirus salmonis in stomach fluid samples taken through the mouth of lumpfish. The established method was based on a previously published real-time PCR assay targeting the mitochondrial cytochrome oxidase I (mtCOI) gene in L. salmonis. Lumpfish were fed with L. salmonis, then captured upon ingestion and subsequently transferred to an incubation tank. The method was used to test 62 fluid samples collected during the first, second and third days post L. salmonis consumption. No DNA extraction or purification was used prior to the real-time PCR. The results were compared with visual examination subsequent to dissection. Visual identification was able to identify 51 L. salmonis (82%) whereas real-time PCR was able to detect 59 L. salmonis (95%) out of the 62 examined samples. The results indicate that real-time PCR assays can be used for specific detection of L. salmonis in fluid samples from the stomach of lumpfish. Furthermore, our study demonstrates that the PCR assay offers a reliable non-lethal alternative to dissection or stomach flushing and the subsequent visual identification of L. salmonis.