This study evaluated the effect of crude oil on the intraradical structures and morphospecies of arbuscular mycorrhizal fungi (AMF) and on the aerial and root dry matter of the grass Leersia hexandra Swartz in order to propose indicators of toxicity. An experiment was conducted in a microtunnel for 180 days. The concentrations (g kg−1) of crude oil in the Gleysol were 0.693 (control), 3, 10, 30, 60, 90, 120, 150, and 180. The growth of intraradical hyphae, arbuscules, vesicles, and spores in soil was stimulated by crude oil concentrations of 3, 10, 30 and 60 g, but concentrations of 90, 120, 150, and 180 g kg−1 inhibited it. Eight morphospecies of AMF were identified. The number of spores of Rhizophagus fasciculatus, Rhizophagus intraradices, Funneliformis geosporum, Diversispora eburnea, and Ambispora gerdemannii showed sensitivity to the concentration of crude oil (index values were lower than one). The number of spores of Diversispora sp. was stimulated by exposure to crude oil, with non-toxic values for the eight concentrations. The index based on the aerial dry matter of L. hexandra showed toxicity values lower than one with crude oil concentrations of 60, 90, 120, 150, and 180 g kg−1, but the root dry matter showed non-toxic values with the eight concentrations. We suggest using the number of spores and morphospecies as an index of toxicity of crude oil and recommend using Diversispora sp. and L. hexandra for the phytoremediation of Gleysol contaminated with crude oil in the Mexican humid tropics.