Technical Abstract: Broiler digestive tract fungal communities have gained far less scrutiny than that given corresponding bacterial communities. Attention given poultry-associated fungi have focused primarily on feed-associated toxin-producers, yeast, and yeast products. The current project focused on the use of pyrosequencing and denaturing gradient gel electrophoresis (DGGE) to identify and monitor broiler digestive fungal communities. Eight treatments included four controls: uninfected-unmedicated, unmedicated-infected, the antibiotic BMD plus the ionophore monensin as positive control, and the ionophore as a negative control. Four treatments included the feed additives: two probiotics, BC-30 and Calsporin, and two specific essential oil blends. All chickens except the unmedicated-uninfected control were given at 15 days of age a standard oral Eimeria inoculum of sporulated oocysts. Ileal and cecal digesta were collected at pre Eimeria infection at 14 days of age and at post Eimeria infection at 22 days of age. Extracted cecal DNA was analyzed by pyrosequencing to examine the impact of diet supplements and Eimeria infection on individual constituents in the fungal community, while DGGE was used to compare more gross changes in ileal and cecal communities. Pyrosequencing identified three phyla, seven classes, eight orders, thirteen families, seventeen genera, and twenty-three fungal species. Ileal and cecal DGGE patterns showed fungal communities were clustered mainly into pre- and post-infection patterns. Post-infection unmedicated-uninfected patterns were clustered with pre-infection groups demonstrating a strong effect of Eimeria infection on digestive fungal populations. These combined techniques offered added versatility towards unraveling the effects of enteropathogen infection and performance enhancing feed additives on broiler digestive microflora.