Management of community diversity of plant-associated arbuscular mycorrhizal fungi (AMF) may be key to the improvement and sustainability of low-input agricultural systems. This research examined the diversity of the indigenous AMF community following an application of turkey litter compost (TLC) and broiler poultry manure (BPM) to a field soil cropped to winter wheat using PCR-denaturing gradient gel electrophoresis (DGGE). By the first fall, 6 months after application of TLC at a rate of 19 T/ha, indigenous soil AMF community diversity was significantly increased compared to the control (no amendment). Additionally, increasing TLC application from 9.5 T/ha to 19 T/ha showed a trend to increase the indigenous AMF community diversity. There were no significant differences in AMF community diversity a year after application of TLC and BPM. This research provides insight into organic amendment effects on soil AMF community diversity which will assist in developing sustainable agricultural practices.