Floor-drains in food, production environments harbour diverse microbes and can be contamination sources. To prevent cross-contamination with spoilage organisms or pathogens, sanitation protocols are regularly applied in food processing facilities. Along with product-associated samples, floor-drain water serves as an important indicator in hygiene monitoring in food processing facilities. However, knowledge about the microbial communities in floor-drains is still low. In this study, the microbial communities in floor-drain water and biofilm samples from an Austrian dairy plant were analysed and revealed that floor-drain microbial communities are dominated by product-associated microbes. DNA was extracted of drain water and drain biofilm samples from three different areas (n = 6) of an Austrian cheese production facility. To characterise the bacterial and eukaryotic communities, 16S rRNA gene pyrosequencing as well as cloning and sequencing of 18S rRNA genes were used. Floor-drain communities were dominated by product-associated bacterial (e.g. Lactobacillus kefiranofaciens, Streptococcus thermophilus) and eukaryotic phylotypes (e.g. Debaryomyces hansenii, Saccharomyces unisporus). In addition, putative drain water derived phylotypes (e.g. Psychrilyobacter atlanticus, Cobetia marina) and ciliates were identified. (C) 2016 Elsevier Ltd. All rights reserved.