Copepods have been found to be a superior live feed for marine larvae compared to moretraditional feed like Artemia and rotifers. This makes them an important food source inaquaculture. However, like every other live feed option, the risk of pathogen transfer to themarine larvae is present. Here, the microbial quality in the process of rearing the copepodAcartia tonsa was assessed. Using the quantitative measures of total cell concentrationand CFU, as well as the qualitative measures of high RNA content, growth potential andfast growing microbes, the microbial quality has been assessed based on r- and K-theory.Haemolytic activity and taxonomy were used to determine the risk of pathogens withinthe process, and bacterial cell contribution from sub-processes was estimated. Microbialcommunity diversity was assessed, using both phenotypic- and genotypic fingerprintingmethods. It was found that the water associated with copepod rearing had an unstableand undetermined selection regime, shifting from r-selection to K-selection. But withoutreaching a stable microbial water quality through the production cycle. The inn-water hadan unfavorable selection regime (r-selection), while the algae reservoir had more favorableK-selection. As the latter contributed to the copepod water with 97-99% of the suppliedmicrobial cells, the selection regime of the inn-water was deemed less important. Dueto limiting analysis methods, the selection regime of the copepods could not be safelydetermined. No heamolytic activity was discovered within the process. The fish pathogenassociated genera Flavobacterium and Tenacibaculum were discovered for A. tonsa andassociated water. However, the absence of haemolytic activity lead to the conclusion thatthe copepods were a good quality live feed choice for marine larvae.