In this study, we focused on the proportion of particular bacterial groups and changes in microbial community structure in relation to the anammox process parameters and the feeding medium strategy in the Sequencing Batch Reactor (SBR). In order to present an insight into the microbial dynamics while feeding medium shift from synthetic wastewater to landfill leachate, fluorescent in situ hybridization (FISH), Real Time PCR, PCR - DGGE (Polymerase Chain Reaction-Denaturing Gradient Gel Electrophoresis) and Reverse Transcription PCR-DGGE analysis were used. Feeding medium change has the strongest impact on relative abundance of denitrifiers and representatives of Planctomycetes. The relative abundancy of specific genes for all investigated nitrogen removal bacterial groups dropped after landfill leachate implementation. However, anammox consortium were able to adapt to the new reactor operating conditions and time for adaptation was estimated at the level of 90 days.