Aflatoxin B1 (AFB1) and zearalenone (ZON) are dangerous mycotoxins due to their carcinogenicity or oestrogenicity. To alleviate negative effects on humans and animals, successful detoxification tools are needed. The application of microorganisms to biodegrade mycotoxins can be an effective way in food and feed industry enhancing food safety. Several Rhodococcus strains are effective in the degradation of aromatic mycotoxins and their application in mycotoxin biodetoxification processes is a promising field of biotechnology. In this study, we investigated the AFB1 and ZON detoxification ability of 42 type strains of Rhodococcus species. Samples were analysed by high-performance liquid chromatograph equipped with fluorescence detector for mycotoxin concentration and SOS-chromotest was used for monitoring remaining genotoxicity. Out of the 42 Rhodococcus strains, 18 could eliminate more than 90% of the applied AFB1 and the genotoxicity was ceased by 15 strains in 72 h (R. imtechensis JCM 13270(T), R. erythropolis JCM 3201(T), R. tukisamuensis JCM 11308(T), R. rhodnii JCM 3203(T), R. aerolatus JCM 19485(T), R. enclensis DSM 45688(T), R. lactis DSM 45625(T), R. trifolii DSM 45580(T), R. qingshengii DSM 45222(T), R. artemisiae DSM 45380(T), R. baikonurensis DSM 44587(T), R. globerulus JCM 7472(T), R. kroppenstedtii JCM 13011(T), R. pyridinivorans JCM 10940(T), R. corynebacterioides JCM 3376(T)). In case of ZON, only R. percolatus JCM 10087(T) was able to degrade more than 90% of the compound and to reduce the oestrogenicity with 70%.