Mercury pollution is an issue of global concern. In Colombia, the use of contaminated water for food crop irrigation and artisanal mining contributes to mercury pollution in soil, affecting food production and restoration of disturbed areas. Mycorrhizal fungi are symbionts that provide benefits to plants including resistance to heavy metals, but fungal effects on germination remain to be fully described. This study tested the effect of mercury and mycorrhizal fungi on Lactuca sativa seed germination. A 2x5 completely randomized factorial experiment was developed to assess the effect of five HgCl2 polluted treatments, two mycorrhizal treatments (i.e., with inoculum, without inoculum), and the interaction of both factors on seed germination, seedling root colonization, pH, and final water content. In samples with no mercury pollution, mycorrhizal fungi had an inhibitory effect on seed germination. Likewise, the effect of mercury on seed germination is significantly inhibitory. However, pots inoculated with arbuscular mycorrhizal fungi showed constant germination probabilities, independently of mercury concentration. According to the best model determined for the data, a key step in the mitigation of mercury toxicity in seed germination is to prevent substrate pH changes. The environmental conditions of the experiment contributed to densely activate populated biomass of inoculum, which promoted root invasion from various points. Overall, the presence of mycorrhizal fungi in seedbeds could lead to a reduced number of plant individuals. However, the use of fungal inoculum in polluted environments, highly contributes to plant establishment, which is relevant in further vegetable cultivations growing in soil polluted areas.