Horses house a dynamic population of microbes within their hindgut that can be disrupted by diet, stress, and medication. Horses are routinely given anthelmintic drugs to reduce internal parasite loads and although their modes of action are well known, there is a lack of knowledge of their effect on the gastrointestinal microflora in horses. The objective of this study was to monitor changes in hindgut microflora after treatment with 2 pyrantel anthelmintic formulations. Ten non-pregnant Quarter Horse mares (8.0 ± 6.0 yr) were randomly assigned to 1 of 2 treatment groups: Paste or Pellet. Throughout the study, all mares continued to receive their basal diet of 0.5% BW of a 12% CP pelleted concentrate with mixed grass hay and water ad libitum. Mares in the Paste group received one dose (0.9 g per 136 kg BW) of pyrantel pamoate paste. Fecal samples were collected immediately before treatment (d 0) and on d 1, 2, 3, 7, 10, and 14 post-treatment. Mares in the Pellet group received pyrantel tartrate pellets (28.3 g per 113 kg bw) once daily for 14 d. Fecal samples were collected immediately before treatment (d 0) and on d 1, 2, 3, 7, 10, and 14 of treatment as well as d 1, 2, 3, 7, 10, and 14 post-treatment. Pooled fecal samples from d 0 served as the untreated controls. DNA was extracted from fecal samples and subjected to PCR-DGGE with universal primers specific to the V2-V3 region of the 16S rRNA gene. PCR-DGGE images were analyzed with BioNumerics software to generate dendrogram comparisons based on the position and number of bands with further evaluation using principal coordinate analysis (PCA). Dendrograms and PCA revealed clustering by time in both groups indicating that pyrantel anthelmintic treatment influenced hindgut microbial diversity. Additional research identifying specific changes in the microbial profiles is needed to better understand the influence of anthelmintic products on the hindgut microflora of horses.