Three methods for extracting DNA were tested on otoliths, scales, fins, and gill tissue from European whitefish [Coregonus lavaratus (L.)]. The aim was to find time-efficient and affordable ways to simultaneously extract DNA suitable for conservation genetic studies from a large number of samples and different tissues. A rapid low-cost method led to 97 % success of microsatellite amplification in otoliths and 100 % in scales. High amplification success was achieved with fin (97 %) and gill (99 %) tissue using a salt lysis-based protocol. A commercial extraction kit delivered good results with all tissues. The findings are useful for conservation genetic studies using both contemporary and archived samples.