Dietary zinc oxide is often used in pharmacological concentrations to promote health as well as performance of weaned piglets due to its bacteriostatic effects. This study was conducted to provide an in depth analysis of the bacterial composition in weaned piglets fed different amounts of dietary zinc oxide. Piglets were fed diets containing 57 (low), 164 (medium) or 2425 (high) mg/kg dietary zinc. Zinc above the basal dietary level was supplied from analytical grade zinc oxide (ZnO). DNA was extracted from stomach and ileum digesta samples of 32 and 53d old animals (n=4 per group) and used to generate bar-coded 16S ribosomal DNA amplicons for deep sequencing analysis. A total of 9 phyla, 40 orders, 75 families and 328 genera were detected in 8.76 x 105 sequencing reads. Firmicutes, Bacteroidetes and Proteobacteria were the dominant phyla, but no significant differences between treatment groups were observed. Lactobacillales (16.3-59.9%), Bacteroidales (2.2-59.1%), Clostridiales (0.05-70.2%) and Selenomonadales (2.6-17.5%) were found as the dominating order. Noteworthy changes on the order level were found for numerically or significantly increased ratios of Clostridiales, but significantly decreased Lactobacillales in the high dietary zinc group. The bacterial diversity for the high dietary zinc diet was significantly higher for the total microbiota than the medium or low zinc diet. However, Lactobacillales diversity decreased, while Clostridiales and Enterobacteriales diversity increased significantly. Principal component analysis confirmed changes in the microbiota, most notably for the high dietary zinc treatment. This study has shown that pharmacological doses of high dietary zinc can drastically alter the bacterial composition and development of the microbiota in weaned piglets. The quantitative shift of bacterial groups due to high dietary zinc was most pronounced one week after weaning, while the more developed microbiota in older animals seemed to be able to adapt to high concentrations of dietary zinc.