In recent decades an increase in the use of pesticides to protect plants from pests, diseases and weeds has been observed. There are many studies on the effects of various pesticides on non-target organisms. This review aims to analyze and summarize published scientific data on the effects of pesticides on the animal microbiome. Pesticides can affect various parameters of the animal microbiome, such as the taxonomic composition of bacteria, bacterial biodiversity, and bacterial ratios and modify the microbiome of various organisms from insects to mammals. Pesticide induced changes in the microbiome reducing the animal’s immunity. The negative effects of pesticides could pose a global problem for pollinators. Another possible negative effect of pesticides is the impact of pesticides on the intestinal microbiota of bumblebees and bees that increase the body’s sensitivity to pathogenic microflora, which leads to the death of insects. In addition, pesticides can affect vitality, mating success and characteristics of offspring. The review considers methods for correcting of bee microbiome.