This study was carried out to assess the effects of exogenous xylanases on production performance and gastrointestinal microbiota of growing gilts fed corn-based or wheat-based diets. A total of 96 individually penned gilts (22.7 ± 0.65 kg initial BW) were used in a CRD experiment with 2 × 6 factorial arrangement and fed experimental diets for 42 d. Gilts (n = 8 per treatment) received one of the 2 basal diets: (a) corn with 40% corn distillers dried grains, or (b) wheat with 25% wheat co-products, each without or with one of the 5 xylanases (XA, XB, XC, XD and XE). Xylanases were supplemented at 75 mg/kg of feed and all diets contained phytase. All xylanases were produced by different fungal organisms, except for xylanase-C, which originated from bacteria. On d 42, all pigs were euthanized to obtain ileal and cecum digesta for microbiome analysis using pyrosequencing of V1-V3 regions of 16S rRNA and downstream bioinformatic analyses using QIIME. Spearman’s correlation was used to correlate microbiome composition data with performance characteristics, apparent total-tract digestibility (ATTD), and colon digesta volatile fatty acids (VFA) concentration. The XA yielded the best growth performance in both corn and wheat based diets (P < 0.05) when compared with other xylanases. Based on PERMANOVA analysis on UniFrac distances, XA significantly affected the β-diversity of ileum microbiota compared with other xylanases and controls (P < 0.05). Furthermore, xylanases influenced ATTD and colonic digester volatile fatty acids diet dependently (P < 0.05). The XA increased Lactobacillus species in the cecum in both diets, whereas other xylanases drastically decreased Lactobacillus species when compared with control (P < 0.05). In the wheat-based diet with xylanases, cecal bacterial community composition changes significantly correlated with ATTD of DM (r = −0.5), gross energy digestibility (r = −0.49) and colon VFA concentrations (r = −0.67) (P < 0.02). However, in the corn-based diet with xylanases, ileal bacterial community changes correlated with ATTD of DM (r = −0.4) and gross energy digestibility (r = −0.43), whereas cecal bacterial community changes correlated with ATTD of fat digestibility (r = −0.58) and colon VFA concentration (r = −0.41) (P < 0.03).