Maraena whitefish (Coregonus maraena; synonym Coregonus lavaretus f. balticus) is a high-quality food fish in the Southern Baltic Sea belonging to the group of salmonid fishes. Coregonus sp. is successfully kept in aquaculture throughout northern Europe (e.g. in Finland, Germany, Russia) and North America. In this regard, the molecular and immunological characterisation of stress response in maraena whitefish contributes to the development of robust and fast-growing maraena whitefish breeding strains for aquaculture. Thus, in the present study, the potential housekeeping genes beta actin (ACTB), elongation factor 1 alpha (EEF1A1), glyceraldehydes-3-phosphate dehydrogenase (GAPDH), ribosomal protein 9 (RPL9), ribosomal protein 32 (RPL32) and ribosomal protein S20 (RPS20) were de novo sequenced and tested concerning their applicability as reference genes in quantitative real-time PCR (qPCR) in maraena whitefish under different stocking densities. For this purpose, tissue samples of liver, kidney, gills, head kidney, skin, adipose tissue, heart and dorsal fin were investigated. qPCR data were analysed with Normfinder tool to determine gene expression stability. DNA sequencing exposed transcribed paralogous EEF1A1A and EEF1A1B genes differing in their putative protein structure. Normfinder analysis revealed RPL9 and RPL32 as most stable, GAPDH and ACTB as least stable genes for qPCR analyses, respectively. This is the first study that provides a subset of seven de novo sequenced housekeeping genes usable as reference genes in studies of stress response in maraena whitefish.