The aim of the study was to analyse the intestinal microbiota of honey bees (Apis mellifera) treated with amitraz. In the present study, the microbiological profile of the honey bee intestines showed minor changes in the microbiota following the application of amitraz. A comparison of the numbers of bacteria and fungi revealed a positive downward trend in the number of fungi. The number of decreased bacteria, includedE. coli and especially Clostridium spp., which were not isolated from the intestines of bees treated with amitraz. The number of lactic acid bacteria before and after treatment was at a similar level of 8.3 log cfu/g of intestinal contents.