Anthropogenic activities have increased the heavy metal (HMs) concentrations in the environment. Taking into consideration that HMs are not biodegradable, they can be accumulated in the soil, absorbed by plants and other living organisms, and later enter the food chains affecting human health. Phytoremediation is an alternative to handle this kind of contamination. Phytoremediation is a low-cost green technology using tolerant plants to remove contaminants from water or soil. Plants used in phytoremediation establish interactions with rhizosphere microorganisms to resist HMs toxicity and increase their phytoextraction capacities. These microorganisms include plant growth-promoting microorganisms, such as bacteria and endophytic fungi, which establish a mutualistic interaction with their hosts. Endophytic microorganisms play a key role in plant growth and development, e.g. they change the soil physicochemical characteristics, mineral and nutrient content, soil waste deposition, and soil water uptake. In addition, plant endophytic bacteria and fungi can remove and/or deactivate contaminants such as HMs through chemical-biological reactions. They contribute to removing contaminants at the rhizosphere which later can be absorbed by plants, which release exudates and enzymes that promote biochemical and microbial activities helping in phytoextraction. This chapter presents a thorough review of updated scientific documents about the interactions of plants with bacteria and/or fungi and their tolerance and absorption of HMs. Also, a deep review of their application in phytoremediation is included.