Diatom contamination is a problem in the early cultivation stages of Saccharina latissima. Macro- and microalgae compete for the same abiotic resources, and diatoms may overgrow and eliminate seedlings of S. latissima if introduced to the macroalgae cultivation system. Germanium dioxide (GeO2), which blocks the cell division in diatoms, has been used as a diatom controller in the growth medium in cultivation of macroalgae. However, the chemical is very expensive and it has been suggested that the chemical inhibit growth of S. latissima seedlings. In the present study, it was desirable to establish a sori disinfection method for large-scale cultivation systems that eliminate diatoms prior to S. latissima spore release. It that was called for a purely chemical disinfection method as mechanical removal of contamination is labour-intensive and costly. Five chemicals, including 130 different trials, were tested on diatoms in free suspension. Acetic acid, sodium hypochlorite and ethanol eliminated diatom growth independent of concentration, exposure time and exposure temperature. Formaldehyde and Lugol’s solution revealed surviving diatoms in the weaker treatments. GeO2 eliminated growth of Chaetoceros muelleri and Skeletonema costatum, but monocultures of Phaeodactylum tricornutum were found at both concentrations (0.1mL L-1 and 0.5mL L-1) eleven days after inoculation. Acetic acid, Lugol’s solution and sodium hypochlorite were tested as sori disinfectants, and GeO2 was used as a negative control for diatom growth. Acetic acid treatments were lethal to both diatoms and S. latissima spores, and GeO2 treatments appeared to have negative influence on fertility and growth of young seedlings of S. latissima. Disinfection with 600ppm sodium hypochlorite or 2% Lugol’s solution, with an exposure time of 2 minutes and exposure temperature of 10°C, followed by two rinsing baths of sterile seawater, gave total elimination of diatoms. No notable effects on spore release, sporophyte growth or early development of young seedling were seen. This implies that disinfection of sori can be done safely by use of these treatments, without concern about reduced quality or quantity of cultivated seaweeds. Sori disinfection was done on disks cut from ripe sori in a disinfecting bath, and no mechanical removal of sori contamination was performed. Sodium hypochlorite was suggested as a new sori disinfectant based on an apparently good safety margin between lethal doses to diatoms and a harmful dose for S. latissima. The chemical also appears to be a widespread disinfectant in aquaculture systems, and can easily be neutralized with thiosulphate.