Objective was to evaluate if uterine microbiota was associated with the presence of fever in metritic cows. Uterine swabs were collected at 6 ± 2 d postpartum (DPP) from 92 cows. Uterine swabs from 11 metritic cows that had a fever (rectal temperature ≥ 39.5°C) at the time of metritis diagnosis (MF), 12 metritic cows that did not have a fever at the time of metritis diagnosis (MNF), and 11 cows that remained healthy (Healthy) were used for metagenomic sequencing of the 16S rRNA gene using the Illumina MiSeq platform. Data were analyzed by ANOVA using the GLM procedure of SAS. Rectal temperature was 38.97 ± 0.12, 38.96 ± 0.08, and 39.89°C ± 0.11 for Healthy, MNF, and MF, respectively. At the phylum level, Bacteroidetes were found to have lower (P < 0.01) relative abundance in Healthy than in MNF and MF (27.3 vs. 51.1 vs. 53.3%), whereas there was no difference (P > 0.25) in Fusobacteria (23.9 vs. 28.6 vs. 24.6%), Actinobacteria (1.2 vs. 0.5 vs. 1.1%), and Firmicutes (18.6 vs. 12.4 vs 15.6). Proteobacteria in Healthy was similar (P = 0.13) to MNF but greater (P = 0.05) than MF (16.6 vs. 6.5 vs. 2.9%). Tenericutes was lower (P < 0.04) in Healthy than in MNF and MF (10.6 vs. 0.7 vs. 2.0%). At the species level, principal coordinates analysis showed that MNF were clustered together with MF, whereas Healthy were mostly separated from metritic cows. Relative abundance of Bacteroides heparinolyticus in Healthy was lower (P = 0.01) than in MNF and tended (P = 0.06) to be lower than in MF (7.0 vs. 20.3 vs. 16.8%). Bacteroides pyogenes was lower (P ≤ 0.05) in Healthy and MNF than in MF (4.0 vs. 3.8 vs. 10.0%), but similar between Healthy and MNF. There was no difference in the relative abundance of Fusobacterium necrophorum (P = 0.68) or other 10 most prevalent bacteria (P > 0.15). In conclusion, Bacteroidetes is more abundant, whereas Firmicutes and Tenericutes are less abundant in metritic cows. Furthermore, B. heparinolyticus is an important species for the development of metritis, whereas B. pyogenes seem to be involved in the development of fever in metritic cows.