Over the past two decades, there has been an alarming decline in the number of honey bee colonies. This phenomenon is called Colony Collapse Disorder (CCD). Bee products play a significant role in human life and have a huge impact on agriculture, therefore bees are an economically important species. Honey has found its healing application in various sectors of human life, as well as other bee products such as royal jelly, propolis, and bee pollen. There are many putative factors of CCD, such as air pollution, GMO, viruses, or predators (such as wasps and hornets). It is, however, believed that pesticides and microorganisms play a huge role in the mass extinction of bee colonies. Insecticides are chemicals that are dangerous to both humans and the environment. They can cause enormous damage to bees’ nervous system and permanently weaken their immune system, making them vulnerable to other factors. Some of the insecticides that negatively affect bees are, for example, neonicotinoids, coumaphos, and chlorpyrifos. Microorganisms can cause various diseases in bees, weakening the health of the colony and often resulting in its extinction. Infection with microorganisms may result in the need to dispose of the entire hive to prevent the spread of pathogens to other hives. Many aspects of the impact of pesticides and microorganisms on bees are still unclear. The need to deepen knowledge in this matter is crucial, bearing in mind how important these animals are for human life.