Fusarium spp. are common fungal pathogens that infect a number of field and vegetable crops.  Crop rotation, genetic resistance, and fungicides are the primary methods used for managing these pathogens.  To date, there is a lack of information regarding the interactions between these management strategies and how they impact Fusarium spp. population dynamics.  The objective of this research was to use real-time polymerase chain reaction (RT-qPCR) to quantify the effect of crop rotation and management (i.e. variety selection and fungicides) on Fusarium spp. (F. graminearum, F. virguliforme, and F. oxysporum) diversity and population dynamics.  Soil was collected in 2011 and 2012 from a long term corn/soybean/wheat rotation study near Arlington, WI.  Previously developed primers for the qPCR were selected based on their specificity for each Fusarium spp.   A qPCR assay and standard curve was optimized for each species using pure culture DNA.  The population for each species (spores g soil^-1) was quantified from extracted soil DNA.  Results suggest that F. oxysporum was the most prevalent Fusarium spp. found.  Crop rotation and management did not have any influence on F. oxysporum populations or F. virguliforme detection.  A crop rotation by fungicide interaction was found for F. graminearum (P < 0.01), but this interaction was mainly affected by crop rotation.  F. graminearum was detected more often in plots with wheat as part of the rotation.  Results from this experiment show RT-qPCR can be a viable tool in helping further understand how to manage these common field crop pathogens.