Bumblebees are one of the most important pollinators for plants consumed by humans. Currently, there is a significant risk of extinction for several pollinators, including bumblebees. One of the most likely causes is the toxic effect of pesticides. The mutagenic effect of pesticides on the DNA of bumblebees has not been studied. The aim of this work was to study the genotoxicity of pesticides for DNA in Bombus terrestris heads. The authors found that if added to bumblebees’ isolated mitochondria, mitochondrial-directed pesticides caused less damage than broad-spectrum pesticides. The greatest amount of mtDNA damage was caused by adding Malathion and Difenoconazole to isolated mitochondria. Moreover, insects that consumed syrup with pesticides displayed more damage to the head than when the pesticide was added to isolated mitochondria. Malathion and Cypermethrin demonstrated significant genotoxic effects in vivo. Difenoconazole caused severe damage to mtDNA, while Deltamethrin did not have any genotoxic effect. Among mitochondria-targeted pesticides, Fenazaquin and Pyridaben demonstrated the highest genotoxicity. Chlorfenapyr, Hydramethylnone, and Tolfenpyrad did not show mtDNA genotoxicity. An increase in the number of copies of mtDNA was observed in insects that consumed sugar syrup with Deltamethrin and Tolfenpyrad. This increase is probably a compensatory effect in response to inhibition of mitochondrial respiration. This study found that, in general, broad-spectrum pesticides (Difenoconazole, Deltamethrin, Esfenvalerate, Malathion, and Cypermethrin) demonstrate greater mtDNA genotoxicity in bumblebees’ heads compared with mitochondria-targeted pesticides (Fenazaquin, Chlorfenapyr, Hydramethylnon, Pyridaben, and Tolfenpyrad).